Extending the quasi-neutral concept

In caricature, the equilibrium paradigm of community ecology states that plant communities are stable entities consisting of competing species - and that such species coexist because each has its “niche”. This paradigm, in its extreme, has been dead for some time. Nevertheless, it has yet to be replaced by a credible “non” — equilibrium paradigm. The quasi-neutral concept of plant communities, proposed by Kristjan Zobel,Folia Geobot. 36: 3–8, 2001, possesses some of the key ingredients of a nonequilibrium theory of diversity. It recognizes that there are inescapable relationships between diversity at different scales, that similarity can influence the rate of competitive exclusion, that successional change is typically associated with changes in life form, and that rarefaction (i.e. “sampling artifacts”) can have strong effects on fine-scale diversity. However, the current formulation of the quasi-neutral concept is incomplete in that it relies on an unrealistic definition of community, it assumes that random sampling means that species richness at one scale will be linearly related to richness at finer scales, it ignores the possibility of fine-scale processes producing broader-scale patterns, and it avoids the subject of fine-scale environmental heterogeneity. But the most serious limitation of the quasi-neutral concept is that similarity of species alone is not sufficient to allow indefinite coexistence. I present the results of a simple simulation to demonstrate that: (1) identical species will eventually be lost from communities due to stochastic “drift”, (2) slight variations in reproductive rates accelerate this loss, but (3) adding a miniscule “cost of commonness” to the model allows the indefinite coexistence of species. I conclude that the quasi-neutral model cannot work without some kind of trade-off.     

Concluding remarks: historical perspective and the future of island biogeography theory

MacArthur and Wilson’s equilibrium theory revolutionized the field of island biogeography and, to a large degree, ecology as well. The theory, which quickly became the ruling paradigm of island biogeography, has changed little over the past three decades. It has not kept pace with relevant theory and our growing appreciation for the complexity of nature, especially with empirical findings that species diversity on many islands: 1) is not in equilibrium; 2) is influenced by differences in speciation, colonization, and extinction among taxa; and 3) is influenced by differences among islands in characteristics other than area and isolation. The discipline of biogeography, itself, is in a state of disequilibrium. We may again be about to witness another paradigm shift, which will see the replacement of MacArthur and Wilson’s theory. Wherever this shift may take us, we are confident that the next generation of biogeographers will still look to islands for insights into the forces that shape biological diversity.     

Islands as model systems in ecology and evolution: prospects fifty years after MacArthur‐Wilson

The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, ‘An equilibrium theory of insular zoogeography’, was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit re‐assessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution – understanding ecosystem functioning, speciation and diversification – frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island‐based theory is continually being enriched, incorporating non‐equilibrium dynamics is identified as a major challenge for the future.     

生态学平衡概念刍议

生态学平衡概念刍议黄富祥刘旭阳（中国科学院植物研究所,北京１０００９３）（湖北大学数学系,武汉４３００６２）ＡｇｒｕｍｅｎｔｓａｂｏｕｔｔｈｅＣｏｎｃｅｐｔｏｆＥｃｏｌｏｇｉｃａｌＥｑｕｉｌｉｂｒｉｕｍ．ＨｕａｎｇＦｕｘｉａｎｇ（Ｉｎｓｔｉｔｕｔｅｏ...     

平衡与非平衡生态学在锡林河流域典型草原放牧系统中的应用

为认识放牧系统的复杂性和稳定性 ,产生了放牧系统的平衡生态学和非平衡生态学原理。放牧系统的平衡生态学原理假定 :一旦干扰在系统中发生 ,系统将偏离平衡态 ;而当干扰解除后 ,系统将自动返回原来的状态或在新的领域实现平衡。在对内蒙古锡林河流域典型草原放牧系统动态的研究中 ,来自平衡生态学的 Clem ents- Duksterhuis演替理论提供了一个基本的研究框架。尽管已经证实对退化不太严重的典型草原放牧系统 ,平衡生态学原理是适用的 ,但是对于这一地区严重退化的放牧系统的动态 ,它显然并不能给予合理的解释。事实上许多放牧系统动态遵循非平衡生态学原理。在非平衡放牧系统中 ,稳定的状态是不会实现的 ,因为在这样的系统中 ,非生物变量对于植被的动态似乎起着决定性的影响 ,从而也决定着草食动物的种群动态。状态与过渡模型基于非平衡生态学原理 ,它能够解释过度放牧下典型草原生态系统的崩溃或灌丛化 ,因此它适于该地区严重退化的典型草原放牧系统的动态。鉴于内蒙古锡林河流域典型草原放牧系统普遍严重退化的现实 ,未来该地退化放牧系统的研究应更多地应用非平衡生态学原理 ,并且严重退化的草原生态系统的恢复试验 ,特别是灌丛化草原的重建也应置于它的指导之下     

The developing relationship between the study of fungal communities and community ecology theory

Plant and animal systems had a head start of several decades in community ecology and have largely created the theoretical framework for the field. I argue that the lag in fungal community ecology was largely due to the microscopic nature of fungi that makes observing species and counting their numbers difficult. Thus the basic patterns of fungal occurrence were, until recently, largely invisible. With the development of molecular methods, especially high-throughput sequencing, fungal communities can now be “seen”, and the field has grown dramatically in response. The results of these studies have given us unprecedented views of fungal communities in novel habitats and at broader scales. From these advances we now have the ability to see pattern, compare it to existing theory, and derive new hypotheses about the way communities are assembled, structured, and behave. But can fungal systems contribute to the development of theory in the broader realm of community ecology? The answer to this question is yes! In fact fungal systems already have contributed, because in addition to many important natural fungal communities, fungi also offer exceptional experimental communities that allow one to manipulate, control, isolate and test key mechanisms. I discuss five well-developed systems and some of the contributions they have made to community ecology, and I briefly mention one additional system that is amenable to development.     

Potential mechanisms of coexistence in closely related forbs

The stable coexistence of very similar species has perplexed ecologists for decades and has been central to the development of coexistence theory. According to modern coexistence theory, species can coexist stably (i.e. persist indefinitely with no long‐term density trends) as long as species' niche differences exceed competitive ability differences, even if these differences are very small. Recent studies have directly quantified niche and competitive ability differences in experimental communities at small spatial scales, but provide limited information about stable coexistence across spatial scales in heterogeneous natural communities. In this study, we use experimental and observational approaches to explore evidence for niche and competitive ability differences between two closely related, ecologically similar and widely coexisting annual forbs: Trachymene cyanopetala and T. ornata. We experimentally tested for stabilizing niche differences and competitive ability differences between these species by manipulating species' frequencies, under both well‐watered and water‐stressed conditions. We considered these experimental results in light of extensive field observations to explore evidence of niche segregation at a range of spatial scales. We found little evidence of intra‐specific stabilization or competitive ability differences in laboratory experiments while observational studies suggested niche segregation across pollinator assemblages and small‐scale microclimate heterogeneity. Though we did not quantify long‐term stabilization of coexisting populations of these species, results are consistent with expectations for stable coexistence of similar species via a spatial storage effect allowing niche differences to overcome even small (to absent) competitive ability differences.     

Effect of Hawk-Dove Game on the Dynamics of Two Competing Species

Outcomes of interspecific competition, and especially the possibility of coexistence, have been extensively studied in theoretical ecology because of their implications in community assemblages. During the last decades, the influence of different time scales through the local/regional dynamics of animal communities has received an increasing attention. Nevertheless, different time scales involved in interspecific competition can result form other processes than spatial dynamics. Here, we envision and analyze a new theoretical framework that couples a game theory approach for competition with a demographic model. We take advantage of these two time scales to derive a reduced model governing the total densities of the two populations and we study how these two time scales interfere and influence outcomes of species competition. We find that a competition process occurring on a faster time scale than demography yields a “priority effect” where the first species introduced outcompetes the other one. We then confirm previous findings stipulating that species coexistence is favored by large difference in time scales because the extinction/recolonization process. Our results then highlight that an integration of demographic and competition time scales at both local and regional levels is mandatory to explain communities assemblages and should become a research priority.     

Compositional turnover in host and parasite communities does not change network structure

Decreasing similarity between ecological communities with increasing geographic distance (i.e. distance‐decay) is a common biogeographical observation in free‐living communities, and a slightly less common observation for parasite communities. Ecological networks of interacting species may adhere to a similar pattern of decreasing interaction similarity with increasing geographic distance, especially if species interactions are maintained across space. We extend this further, examining if host–parasite networks – independent of host and parasite species identities – become more structurally dissimilar with increasing geographic distance. Utilizing a global database of helminth parasite occurrence records, we find evidence for distance‐decay relationships in host and parasite communities at both regional and global scales, but fail to detect similar relationships in network structural similarity. Host and parasite community similarity were strongly related, and both decayed rapidly with increasing geographic distance, typically resulting in complete dissimilarity after approximately 2500 km. Our failure to detect a decay in network structural similarity suggests the possibility that different host and parasite species are filling the same functional roles in interaction networks, or that variation in network similarity may be better explained by other geographic variables or aspects of host and parasite ecology.     

Interactions matter—complexity in landscapes and ecosystems

In this review we argue that theories and methodology arising from the field of complex systems form a new paradigm for ecology. Patterns and processes resulting from interactions between individuals, populations, species and communities in landscapes are the core topic of ecology. These interactions form complex networks, which are the subject of intense research in complexity theory, informatics and statistical mechanics. This research has shown that complex natural networks often share common structures such as loops, trees and clusters. The observed structures contribute to widespread processes including feedback, non-linear dynamics, criticality and self-organisation. Simulation modelling is a key tool in studying complex networks and has become popular in ecology, especially in adaptive management. Important techniques include cellular automata and individual-based models. The complex systems paradigm has led to advances in landscape ecology, including a deeper understanding of the dynamics of spatial pattern formation, habitat fragmentation, epidemic processes, and genetic variation. Network analysis reveals that underlying patterns of interactions, such as small worlds and clusters, in food webs and ecosystems have strong implications for their stability and dynamics. These investigations illustrate how complexity theory and associated methodologies are transforming ecological research, providing new perspectives on old questions as well as raising many new ones.     

Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales

Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance vs. host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree—including tree age, size and soil chemistry—and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modelling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free‐living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity—and, surprisingly, not host species—were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil‐mediated systems.     

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.     

A metabolic view of amphibian local community structure: the role of activation energy

In the context of the metabolic theory of ecology (MTE), the activation energy (E) reflects the temperature dependence of metabolism and organism performance in different activities, such as calling behavior. In this contribution we test the role of temperature in affecting local amphibian community structure, particularly the number of species engaged in calling behavior across a temperature gradient. Toward this aim, we compiled phenological calling activity for 52 Neotropical anuran communities. For each community we estimated the activation energy of calling behavior (E), finding values significantly higher than previous reports. A wide range of methodological issues with the potential to produce overestimated E‐values were shown to have no significant effect on reported E‐values, supporting a biological interpretation of their high values and of geographic trends. Further, a path analysis related variation in E among communities with communities’ phylogenetic structure, local environmental conditions, richness, and seasonality. The decrease of activation energy at higher latitudes and less productive environments suggests that amphibians’ activity could become more dependent of internal individuals’ resources once external sources are reduced. The increase in phylogenetic attraction with latitude points to a rise in the role of niche conservatism and community filtering operating over conserved traits. Finally, flexibility in activation energy related to amphibians’ calling could be an important and poorly recognized determinant of their thermal dependence. The temporal structuring of amphians’ communities was related here with the interplay between ecological and evolutionary processes operating at different scales. Our results support the view of activation energy as an important parameter of biodiversity organization, which unravels the effects of ecological and evolutionary processes on biodiversity structure and function.     

Biodiversity as insurance: from concept to measurement and application

Biological insurance theory predicts that, in a variable environment, aggregate ecosystem properties will vary less in more diverse communities because declines in the performance or abundance of some species or phenotypes will be offset, at least partly, by smoother declines or increases in others. During the past two decades, ecology has accumulated strong evidence for the stabilising effect of biodiversity on ecosystem functioning. As biological insurance is reaching the stage of a mature theory, it is critical to revisit and clarify its conceptual foundations to guide future developments, applications and measurements. In this review, we first clarify the connections between the insurance and portfolio concepts that have been used in ecology and the economic concepts that inspired them. Doing so points to gaps and mismatches between ecology and economics that could be filled profitably by new theoretical developments and new management applications. Second, we discuss some fundamental issues in biological insurance theory that have remained unnoticed so far and that emerge from some of its recent applications. In particular, we draw a clear distinction between the two effects embedded in biological insurance theory, i.e. the effects of biodiversity on the mean and variability of ecosystem properties. This distinction allows explicit consideration of trade-offs between the mean and stability of ecosystem processes and services. We also review applications of biological insurance theory in ecosystem management. Finally, we provide a synthetic conceptual framework that unifies the various approaches across disciplines, and we suggest new ways in which biological insurance theory could be extended to address new issues in ecology and ecosystem management. Exciting future challenges include linking the effects of biodiversity on ecosystem functioning and stability, incorporating multiple functions and feedbacks, developing new approaches to partition biodiversity effects across scales, extending biological insurance theory to complex interaction networks, and developing new applications to biodiversity and ecosystem management.     

尺度与密度:测定不同尺度下的种群密度

群落中的种群密度由于空间尺度的变化而存在着一定差异,那么,某一种群的密度随着空间尺度的变化会发生怎样的变化?抑或某一物种相对于另一物种而言,随着空间尺度的变化其密度会怎样变化?这是与尺度有关的种群密度问题,当属生态学的基本问题.该文提出这样的问题,并把不同尺度下的种群密度称之为尺度密度(scale density).O-Ring函数的实质是计算不同尺度下的种群密度.因此,在研究实例中,应用O-Ring函数计算了典型草原处于不同恢复阶段的羊草(Leymuschinensis)种群、米氏冰草(Agropyron michnoi)种群,以及米氏冰草种群相对于羊草种群在不同尺度下的种群密度,结果发现:羊草和米氏冰草2个种群的尺度密度,在小尺度范围内严重退化群落均高于恢复演替群落,这一结果验证了“胁迫梯度假说”,同时表明该结果是放牧胁迫下正相互作用所致;通过比较羊草种群与米氏冰草相对于羊草的尺度密度发现,在严重退化的群落中,羊草与米氏冰草的种间关联为负联结,这种负联结是由正相互作用引起的,而在恢复8年和恢复21年群落中,二者之间是正联结,当为竞争所致.该实例说明分析种群密度随尺度变化的规律对于深入认识生态学问题可能会有很大帮助.     

Overdispersion of body size in Australian desert lizard communities at local scales only: no evidence for the Narcissus effect

Both local and regional processes may contribute to community diversity and structure at local scales. Although many studies have investigated patterns of local or regional community structure, few have addressed the extent to which local community structure influences patterns within regional species pools. Here we investigate the role of body size in community assembly at local and regional scales in Ctenotus lizards from arid Australia. Ctenotus has long been noted for its exceptional species diversity in the Australian arid-zone, and previous studies have attempted to elucidate the processes underlying species coexistence within communities of these lizards. However, no consensus has emerged on the role of interspecific competition in the assembly and maintenance of Ctenotus communities. We studied Ctenotus communities at several hundred sites in the arid interior of Australia to test the hypothesis that body sizes within local and regional Ctenotus assemblages should be overdispersed relative to null models of community assembly, and we explored the relationship between body size dispersion at local and regional scales. Results indicate a striking pattern of community-wide overdispersion of body size at local scales, as measured by the variance in size ratios among co-occurring species. However, we find no evidence for body size overdispersion within regional species pools, suggesting a lack of correspondence between processes influencing the distribution of species phenotypes at local and regional scales. We suggest that size ratio constancy in Ctenotus communities may have resulted from contemporary ecological interactions among species or ecological character displacement, and we discuss alternative explanations for the observed patterns. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Tree size distributions in an old-growth temperate forest

Despite the wide variation in the structural characteristics in natural forests, tree size distribution show fundamental similarities that suggest general underlying principles. The metabolic ecology theory predicts the number of individual scales as the −2 power of tree diameter. The demographic equilibrium theory predicts tree size distribution starting from the relationship of size distributions with growth and mortality at demographic equilibrium. Several analytic predictions for tree size distributions are derived from the demographic equilibrium theory, based on different growth and mortality functions. In addition, some purely phenomenological functions, such as polynomial function, have been used to describe the tree size distributions. In this paper, we use the metabolic ecology theory, the demographic equilibrium theory and the polynomial function to predict the tree size distribution for both the whole community and each species in an old-growth temperate forest in northeastern China. The results show that metabolic ecology theory predictions for the scaling of tree abundance with diameter were unequivocally rejected in the studied forest. Although these predictions of demographic theory are the best models for most of the species in the temperate forest, the best models for some species ( Tilia amurensis , Quercus mongolica and Fraxinus mandshurica ) are compound curves (i.e. rotated sigmoid curves), best predicted by the polynomial function. Hence, the size distributions of natural forests were unlikely to be invariant and the predictive ability of general models was limited. As a result, developing a more sophisticated theory to predict tree size distributions remains a complex, yet tantalizing, challenge.     

Fifteen important questions in the spatial ecology of diatoms

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Scale,succession and complexity in island biogeography: are we asking the right questions?

• 1 This paper offers a commentary on the development of island ecological theory since the publication of MacArthur & Wilson’s equilibrium theory in the 1960s. I distinguish the simple model at the core of their Equilibrium Theory of Island Biogeography (ETIB) and the broader body of their theory, which embraces evolutionary as well as ecological patterns — all, however, within the overarching framework or assumption of equilibrium.
• 2 The basic problems with the ETIB have long been known, and its status as a ruling paradigm has been the subject of concern for more than two decades. With the development of nonequilibrium ideas in ecology, island biogeographers arguably now have viable theoretical frameworks to set alongside or around the ETIB. Four conditions are highlighted as extremes: i) dynamic equilibrium; ii) dynamic nonequilibrium; iii) ‘static’ equilibrium; and iv) ‘static’ nonequilibrium: together providing a conceptual framework for island ecological analyses.
• 3 The importance of scale is stressed and attention is drawn to Haila’s spatial‐temporal continuum as an organizational device. It is argued that the processes represented within the ETIB (and by extension, other island theories) may be prominent within only a limited portion of this continuum, while elsewhere they are generally subsumed by other dominant processes.
• 4 Colonization and ecosystem development of near‐shore islands constitute just a special case of ecological succession, and thus the development of theories of island assembly may benefit accordingly from efforts to incorporate ideas from the ecological succession literature.
• 5 The desirability of specifying answerable questions is stressed, as is the need to build a greater degree of complexity into the development of island ecological models. Notwithstanding which, it is also recognized that key advances are often brought about by simple, but bold models, of the form exemplified elsewhere in this issue.