The importance of niche differentiation for coexistence on large scales

It is widely accepted that niche differentiation plays a key role in coexistence on relatively small scales. With regard to a large community scale, the recently propounded neutral theory suggests that species abundances are more influenced by history and chance than they are by interspecies competition. This inference is mainly based on the probability that competitive exclusion is largely slowed by recruitment limitation, which may be common in species rich communities. In this respect, a theoretical study conducted by Hurtt and Pacala (1995) for a niche differentiated community has been frequently cited to support neutral coexistence. In this paper, we focused on the effect of symmetric recruitment limitation on delaying species competitive exclusion caused by both symmetric and asymmetric competition in a large homogeneous habitat. By removing niche differentiation in space, we found that recruitment limitation could delay competitive exclusion to some extent, but the effect was rather limited compared to that predicted by Hurtt and Pacala's model for a niche differentiated community. Our results imply that niche differentiation may be important for species coexistence even on large scales and this has already been confirmed in some species rich communities.     

When can we distinguish between neutral and non‐neutral processes in community dynamics under ecological drift?

Determining whether the composition of ecological communities (species presence and abundance), can be predicted from species demographic traits, rather than being a result of neutral drift, is a key ecological question. Here we compare the similarity of community composition, from different community assembly models run under identical environmental conditions, where interspecific competition is assumed to be either neutral or niche-based. In both cases, species colonize a focal patch from a network of neighbouring patches in a metacommunity. We highlight the circumstances (rate and spatial scale of dispersal, and the relative importance of ecological drift) where commonly used community similarity metrics or species rank–abundance relationships are likely to give similar results, regardless of the underlying processes (neutral or non-neural) driving species' dynamics. As drift becomes more important in driving species abundances, deterministic niche structure has a smaller influence. Our ability to discriminate between different underlying processes driving community organization depends on the relative importance of different drift processes that operate on different spatial scales.     

植物群落构建机制研究进展

群落构建研究对于解释物种共存和物种多样性的维持是至关重要的,因此一直是生态学研究的中心论题。尽管近年来关于生态位和中性理论的验证研究已经取得了显著的成果,但对于局域群落构建机制的认识仍存在很大争议。随着统计和理论上的进步使得用功能性状和群落谱系结构解释群落构建机制变为可能,主要是通过验证共存物种的性状和谱系距离分布模式来实现。然而,谱系和功能性状不能相互替代,多种生物和非生物因子同时控制着群落构建,基于中性理论的扩散限制、基于生态位的环境过滤和竞争排斥等多个过程可能同时影响着群落的构建。所以,综合考虑多种方法和影响因素探讨植物群落的构建机制,对于预测和解释植被对干扰的响应,理解生物多样性维持机制有重要意义。试图在简要回顾群落构建理论及研究方法发展的基础上,梳理其最新研究进展,并探讨整合功能性状及群落谱系结构的研究方法,解释群落构建和物种多样性维持机制的可能途径。在结合功能性状和谱系结构研究群落构建时,除了考虑空间尺度、环境因子、植被类型外,还应该关注时间尺度、选择性状的种类和数量、性状的种内变异、以及人为干扰等因素对群落构建的影响。     

Stable isotope analyses reveal dense trophic species packing and clear niche differentiation in a malagasy primate community

Understanding the mechanisms maintaining local species richness is a major topic in tropical ecology. In ecological communities of Madagascar, primates represent a major part of mammalian diversity and, thus, are a suitable taxon to study these mechanisms. Previous research suggested that ecological niche differentiation facilitates the coexistence of lemurs. However, detailed data on all species making up diverse local primate assemblages is rarely available, hampering community‐wide tests of niche differentiation among Malagasy mammals. Here, we took an indirect approach and used stable isotopes as long‐term indicators of individuals' diets to answer the question of whether trophic patterns and food‐related mechanisms stabilize coexistence in a species‐rich lemur community. We analyzed stable carbon and nitrogen isotopes in hair collected from eight syntopic lemurs in Kirindy Forest. We found that lemur species were well separated into trophic niches and ranged over two trophic levels. Furthermore, species were densely packed in isotopic space suggesting that past competitive interactions between species are a major structuring force of this dry forest lemur community. Results of other comparative studies on primates and our findings underline that—in contrast to communities worldwide—the structure and composition of lemur communities follow predictions of ecological niche theory. Patterns of competitive interactions might be more clearly revealed in Malagasy primate communities than elsewhere because lemurs represent a large fraction of ecologically interacting species in these communities. The pronounced trophic niche differentiation among lemurs is most likely due to intense competition in the past as is characteristic for adaptive radiations. Am J Phys Anthropol 153:249–259, 2014. © 2013 Wiley Periodicals, Inc.     

Assembly rules for New England ant assemblages

Community assembly rules specify patterns of species co-occurrence and morphology dictated by interspecific competition. We collected data on the occurrence of ground-foraging ant species in 22 ombrotrophic bogs and adjacent forest plots of New England to test two general assembly rules: reduced co-occurrence of species among communities, and even spacing of body sizes of species within communities. We used null models to generate random communities unstructured by competition and evaluated patterns at regional and local spatial scales. At the regional scale, species co-occurrence in forests, but not bogs, was less than expected by chance, whereas, at the local scale, co-occurrence in both habitats was not different from random. At the regional scale, spacing of body size distributions was random (in bogs) or aggregated (in forests). At the local scale, body size patterns were weakly segregated in bogs, but random or weakly aggregated in forests. In bogs, size ratio constancy was accompanied by greater generic diversity than expected. Although assembly rules were originally developed for vertebrate communities, they successfully explained some patterns in New England ant assemblages. However, the patterns were contingent on spatial scale, and were distinctly different for bog and forest communities, despite their close proximity and the presence of many shared species in both assemblages. The harsh physical conditions of bogs may act as a habitat filter that alters community assembly rules.     

Scaling coexistence and assemblage patterns of desert small mammals

Scaling biodiversity patterns has been recognized lately as a very important issue in the search of global processes; however coexistence and assemblage patterns are typically approached at a single spatial scale. Here, we examined coexistence and co-occurrence patterns of desert small mammal communities across different spatial scales in the search of general community patterns. We sampled small mammals in Monte desert (Argentina, South America) for small spatial scales and reviewed published papers from other worldwide deserts for large spatial scale analyses. We used classic community estimators (Shannon, Richness), rank abundance curves and fitting distributions to analyze species coexistence and co-occurrence patterns. Assemblage patterns were analyzed evaluating nestedness across spatial scales and among deserts. Worldwide desert small mammal assemblages are characterized mainly by low species richness and high variation in species composition. The central Monte desert of Argentina showed a consistent assemblage pattern across spatial scales, with a generalist species being the most abundant and widely distributed, accompanied by other subordinate and more narrowly distributed species. All Monte desert communities were significantly nested, with nestedness increasing with scale from patch to regional. Assemblage and coexistence patterns were similar when comparing worldwide deserts despite differences in total richness and faunal singularity. The degree of nestedness varied among worldwide deserts; however all of them showed a consistent nested pattern. Differences in the degree of nestedness could be a result of different regulating factors depending on the desert and scale. These results highlight the importance of including multiscale approaches when dealing with processes that structure desert communities.     

Community assembly and diversification in Indo-Pacific coral reef fishes

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model.     

Concurrent niche and neutral processes in the competition-colonization model of species coexistence

The importance of neutral dynamics is contentiously debated in the ecological literature. This debate focuses on neutral theory's assumption of fitness equivalency among individuals, which conflicts with stabilizing fitness that promotes coexistence through niche differentiation. I take advantage of competition-colonization trade-offs between species of aquatic micro-organisms (protozoans and rotifers) to show that equalizing and stabilizing mechanisms can operate simultaneously. Competition trials between species with similar colonization abilities were less likely to result in competitive exclusion than for species further apart. While the stabilizing mechanism (colonization differences) facilitates coexistence at large spatial scales, species with similar colonization abilities also exhibited local coexistence probably due to fitness similarities allowing weak stabilizing mechanisms to operate. These results suggest that neutral- and niche-based mechanisms of coexistence can simultaneously operate at differing temporal and spatial scales, and such a spatially explicit view of coexistence may be one way to reconcile niche and neutral dynamics.     

Spatial constraints masking community assembly rules: A simulation study

The effect of competition on species coexistence is usually strongly modified by other factors especially in non-equilibrium systems of sessile organisms with limited availability of propagules. As a consequence, competition-based assembly rules (even if their existence seems to be unambiguously detected) would result in incomplete understanding of the coexistence of species in plant communities. J. Bastow Wilson suggested measuring variance deficit in the number of co-occurring species as a means to detect niche limitation in a community. The method provides a relatively simple and quick “snap-shot” analysis of a community. However, it has been questioned whether niche limitation is the only factor which might account for variance deficit. The paper presents a spatially explicit simulation experiment in which artificial communities are produced by pre-defined rules for competitive interactions. Then we examine whether these rules can be detected by a proposed method for pattern analysis. Two limiting cases are simulated: (A) all the species share the same niche, and (B) all the species have different niches. The difference between these cases in the variance of species numbers is examined. Using the simulation results, some basic spatial constraints upon species assembly are emphasized. It is argued that the assumptions of Wilson’s approach confine its applicability to species-saturated equilibrium communities. The study of assembly rules in dynamically changing, spatially structured communities requires the consideration of a set of coenological characteristics and the use of careful spatio-temporal scaling to detect their patterns. The use of spatially explicit individual-based models to study the mechanisms and constraints limiting species coexistence at different scales is suggested.     

草地群落物种多样性维持机制的研究Ⅱ物种实现的生态位

尽管为解释种类丰富的植物群落物种共存和多样性维持机制,生态学家位做了大量的努力并提出了许多假说和模型。但这一问题仍处在争议之中,需要更多的证据支持他们的观点或提出新的看法,使这一生物多样性难题不断地向前推进。以松赖平原物种丰富度较高的羊草－杂类草群落为对象,在土壤C、N、P、K和H2O等5个资源轴上,探讨了物种多样性与实现生态位的关系。结果表明：尽管物种生态位存在一定程度的分化,但多数物种的生态位是高度重叠的,物种生态位的分化在草地群落物种共存和多样性维持中,不是唯一的途径,认为应更加重视的物种在长期协同进化中所形成的生物学特性。     

Coexistence via resource partitioning fails to generate an increase in community function

Classic ecological theory suggests that resource partitioning facilitates the coexistence of species by reducing inter-specific competition. A byproduct of this process is an increase in overall community function, because a greater spectrum of resources can be used. In contrast, coexistence facilitated by neutral mechanisms is not expected to increase function. We studied coexistence in laboratory microcosms of the bactivorous ciliates Paramecium aurelia and Colpidium striatum to understand the relationship between function and coexistence mechanism. We quantified population and community-level function (biomass and oxygen consumption), competitive interactions, and resource partitioning. The two ciliates partitioned their bacterial resource along a size axis, with the larger ciliate consuming larger bacteria than the smaller ciliate. Despite this, there was no gain in function at the community level for either biomass or oxygen consumption, and competitive effects were symmetrical within and between species. Because other potential coexistence mechanisms can be ruled out, it is likely that inter-specific interference competition diminished the expected gain in function generated by resource partitioning, leading to a system that appeared competitively neutral even when structured by niche partitioning. We also analyzed several previous studies where two species of protists coexisted and found that the two-species communities showed a broad range of biomass levels relative to the single-species states.     

Co-occurrence Patterns along a Regional Aridity Gradient of the Subtropical Andes Do Not Support Stress Gradient Hypotheses

The stress gradient hypothesis posits that facilitation and stress are positively correlated. The hump-shaped hypothesis, on the contrary, proposes that facilitation is greater at intermediate stress levels. The relationship between facilitation and environmental stress is commonly studied at small spatial scales and/or considering few species; thus, the implications of facilitation at a community level remain poorly understood. Here, we analyzed local co-occurrence patterns of all plant species at 25 sites within the subtropical Andes to evaluate the role of facilitation and competition as drivers of community structure. We considered a wide latitudinal gradient (19–26°S) that incorporates great variation in aridity. No previous studies have attempted to study these patterns across such a broad scale in warm deserts. Each locality was sampled at two scales (quadrat and patch), and co-occurrence was analyzed via null models. Furthermore, we tested for a relationship between plant co-occurrences and environmental aridity. Resulting patterns depended on life form. When all species were considered, negative associations were found, indicating competition. Woody/cactus life forms tended to be associated across communities, suggesting that there is facilitation between these life forms. Additionally, and unlike previous studies, we found positive associations among shrubs. The strength of the association between woody species changed non-monotonically with aridity. Herbs showed an inverted hump-shaped relationship, albeit ranging mostly among neutral values. Independent of the association type exhibited by different life forms, our community level results do not support current stress gradient hypotheses.     

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world’s largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

     

Competitive intransitivity promotes species coexistence

Using a spatially explicit cellular automaton model with local competition, we investigate the potential for varied levels of competitive intransitivity (i.e., nonhierarchical competition) to promote species coexistence. As predicted, on average, increased levels of intransitivity result in more sustained coexistence within simulated communities, although the outcome of competition also becomes increasingly unpredictable. Interestingly, even a moderate degree of intransitivity within a community can promote coexistence, in terms of both the length of time until the first competitive exclusion and the number of species remaining in the community after 500 simulated generations. These results suggest that modest levels of intransitivity in nature, such as those that are thought to be characteristic of plant communities, can contribute to coexistence and, therefore, community-scale biodiversity. We explore a potential connection between competitive intransitivity and neutral theory, whereby competitive intransitivity may represent an important mechanism for "ecological equivalence."     

Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines

Dispersal among local communities can have a variety of effects on species composition and diversity at local and regional scales. Local conditions (e.g., resource and predator densities) can have independent effects, as well as interact with dispersal, to alter these patterns. Based on metacommunity models, we predicted that local diversity would show a unimodal relationship with dispersal frequency. We manipulated dispersal frequencies, resource levels, and the presence of predators (mosquito larvae) among communities found in the water-filled leaves of the pitcher plant Sarracenia purpurea. Diversity and abundance of species of the middle trophic level, protozoa and rotifers, were measured. Increased dispersal frequencies significantly increased regional species richness and protozoan abundance while decreasing the variance among local communities. Dispersal frequency interacted with predation at the local community scale to produce patterns of diversity consistent with the model. When predators were absent, we found a unimodal relationship between dispersal frequency and diversity, and when predators were present, there was a flat relationship. Intermediate dispersal frequencies maintained some species in the inquiline communities by offsetting extinction rates. Local community composition and the degree of connectivity between communities are both important for understanding species diversity patterns at local and regional scales.     

Compositional divergence and convergence in local communities and spatially structured landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.     

Local community size mediates ecological drift and competition in metacommunities

The outcome of competitive interactions is likely to be influenced by both competitive dominance (i.e. niche-based dynamics) and ecological drift (i.e. neutral dynamics governed by demographic stochasticity). However, spatial models of competition rarely consider the joint operation of these two processes. We develop a model based on the original competition-colonization trade-off model that incorporates niche and neutral processes and several realistic facets of ecological dynamics: it allows local competition (i.e. competition within a patch) to occur within communities of a finite size, it allows competitors to vary in the degree of competitive asymmetry, and it includes the role of local migration (i.e. propagule pressure). The model highlights the role of community size, i.e. the number of competitors in the local community, in mediating the relative importance of stochastic and deterministic forces. In metacommunities where local communities are small, ecological drift is substantial enough that strong competitors become effectively neutral, creating abrupt changes in the outcome of competition not predicted by the standard competition-colonization trade-off. Importantly, the model illustrates that, even when other aspects of species interactions (e.g. migration ability, competitive ability) are unchanged, local community size can alter the dynamics of metacommunity persistence. Our work demonstrates that activities which reduce the size of local communities, such as habitat destruction and degradation, effectively compound the extinction debt.     

Untangling the mechanisms of cryptic species coexistence in a nematode community through individual-based modelling

Cryptic species are morphologically identical but genetically distinct, and are prominent across numerous phyla. The coexistence of such closely related species on local scales would seem to run counter to traditional coexistence and competition theory; it has been hypothesized as a consequence of differences in their resource use or tolerances to environmental conditions. We developed an individual-based model of a community of three cryptic Litoditis marina (nematode) species, to understand how individual-level interspecific and intraspecific interactions might explain the coexistence of these closely related species. The model incorporates individuals' reproduction, competition, dispersal and resource use. Data characterizing the cryptic species (growth rates, dispersal ability, competitive interactions and responses to changing environmental conditions) were obtained from laboratory experiments involving both mono- and multispecific nematode cultures, and are used to parameterize the model. Simulation studies are used to investigate which individual-level mechanisms of dispersal and interaction lead to the characteristic population-level patterns observed experimentally. Our results highlight the key role of intraspecific competition in mediating dispersal and therefore co-occurrence of the cryptic species. The differences in dispersal also influence the response of the cryptic species to competition, a combination of factors that provides an explanation for their co-occurrence. These results provide insights into how changes in individual-level processes can be amplified to affect population-level co-occurrence.     

A minimum stochastic model evaluating the interplay between population density and drift for species coexistence

Despite the general acknowledgment of the role of niche and stochastic process in community dynamics, the role of species relative abundances according to both perspectives may have different effects regarding coexistence patterns. In this study, we explore a minimum probabilistic stochastic model to determine the relationship of populations relative and total abundances with species chances to outcompete each other and their persistence in time (i.e., unstable coexistence). Our model is focused on the effects drift (i.e., random sampling of recruitment) under different scenarios of selection (i.e., fitness differences between species). Our results show that taking into account the stochasticity in demographic properties and conservation of individuals in closed communities (zero-sum assumption), initial population abundance can strongly influence species chances to outcompete each other, despite fitness inequalities between populations, and also, influence the period of coexistence of these species in a particular time interval. Systems carrying capacity can have an important role in species coexistence by exacerbating fitness inequalities and affecting the size of the period of coexistence. Overall, the simple stochastic formulation used in this study demonstrated that populations initial abundances could act as an equalizing mechanism, reducing fitness inequalities, which can favor species coexistence and even make less fitted species to be more likely to outcompete better-fitted species, and thus to dominate ecological communities in the absence of niche mechanisms. Although our model is restricted to a pair of interacting species, and overall conclusions are already predicted by the Neutral Theory of Biodiversity, our main objective was to derive a model that can explicitly show the functional relationship between population densities and community mono-dominance odds. Overall, our study provides a straightforward understanding of how a stochastic process (i.e., drift) may affect the expected outcome based on species selection (i.e., fitness inequalities among species) and the resulting outcome regarding unstable coexistence among species.     

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.