Reconciling empirical ecology with neutral community models

Neutral community models embody the idea that individuals are ecologically equivalent, having equal fitness over all environmental conditions, and describe how the spatial dynamics and speciation of such individuals can produce a wide range of patterns of distribution, diversity, and abundance. Neutral models have been controversial, provoking a rush of tests and comments. The debate has been spurred by the suggestion that we should test mechanisms. However, the mechanisms and the spatial scales of interest have never clearly been described, and consequently, the tests have often been only peripherally relevant. At least two mechanisms are present in spatially structured neutral models. Dispersal limitation causes clumping of a species, which increases the strength of intraspecific competition and reduces the strength of interspecific competition. This may prolong coexistence and enhance local and regional diversity. Speciation is present in some neutral models and gives a donor-controlled input of new species, many of which remain rare or are short lived, but which directly add to species diversity. Spatial scale is an important consideration in neutral models. Ecological equivalence and equal fitness have implicit spatial scales because dispersal limitation and its emergent effects operate at population levels, and populations and communities are defined at a chosen spatial scale in recent neutral models; equality is measured relative to a metacommunity, and this necessitates defining the spatial scale of that metacommunity. Furthermore, dispersal has its own scales. Thorough empirical tests of neutral models will require both tests of mechanisms and pattern-producing ability, and will involve coupling theoretical models and experiments.     

A nearly neutral model of biodiversity

S. P. Hubbell's unified neutral theory of biodiversity has stimulated much new thinking about biodiversity. However, empirical support for the neutral theory is limited, and several observations are inconsistent with the predictions of the theory, including positive correlations between traits associated with competitive ability and species abundance and correlations between species diversity and ecosystem functioning. The neutral theory can be extended to explain these observations by allowing species to differ slightly in their competitive ability (fitness). Here, we show that even slight differences in fecundity can greatly reduce the time to extinction of competitors even when the community size is large and dispersal is spatially limited. In this case, species richness is dramatically reduced, and a markedly different species abundance distribution is predicted than under pure neutrality. In the nearly neutral model, species co-occur in the same community not because of, but in spite of, ecological differences. The more competitive species with higher fecundity tend to have higher abundance both in the metacommunity and in local communities. The nearly neutral perspective provides a theoretical framework that unites the sampling model of the neutral theory with theory of biodiversity affecting ecosystem function.     

Characterizing species abundance distributions across taxa and ecosystems using a simple maximum entropy model

The species abundance distribution (SAD) is one of themost studied patterns in ecology due to its potential insights into commonness and rarity, community assembly, and patterns of biodiversity. It is well established that communities are composed of a few common and many rare species, and numerous theoretical models have been proposed to explain this pattern. However, no attempt has been made to determine how well these theoretical characterizations capture observed taxonomic and global-scale spatial variation in the general form of the distribution. Here, using data of a scope unprecedented in community ecology, we show that a simple maximum entropy model produces a truncated log-series distribution that can predict between 83% and 93% of the observed variation in the rank abundance of species across 15 848 globally distributed communities including birds, mammals, plants, and butterflies. This model requires knowledge of only the species richness and total abundance of the community to predict the full abundance distribution, which suggests that these factors are sufficient to understand the distribution for most purposes. Since geographic patterns in richness and abundance can often be successfully modeled, this approach should allow the distribution of commonness and rarity to be characterized, even in locations where empirical data are unavailable.     

Leaf quality, predators, and stochastic processes in the assembly of a diverse herbivore community

Ecological communities are structured by both deterministic, niche-based processes and stochastic processes such as dispersal. A pressing issue in ecology is to determine when and for which organisms each of these types of processes is important in community assembly. The roles of deterministic and stochastic processes have been studied for a variety of communities, but very few researchers have addressed their contribution to insect herbivore community structure. Insect herbivore niches are often described as largely shaped by the antagonistic pressures of predation and host plant defenses. However host plants are frequently discrete patches of habitat, and their spatial arrangement can affect herbivore dispersal patterns. We studied the roles of predation, host plant quality, and host spatial proximity for the assembly of a diverse insect herbivore community on Quercus alba (white oak) across two growing seasons. We examined abundances of feeding guilds to determine if ecologically similar species responded similarly to variation in niches. Most guilds responded similarly to leaf quality, preferring high-nitrogen, low-tannin host plants, particularly late in the growing season, while bird predation had little impact on herbivore abundance. The communities on the high-quality plants tended to be larger and, in some cases, have greater species richness. We analyzed community composition by correlating indices of community similarity with predator presence, leaf quality similarity, and host plant proximity. Birds did not affect community composition. Community similarity was significantly associated with distance between host plants and uncorrelated with leaf quality similarity. Thus although leaf quality significantly affected the total abundance of herbivores on a host plant, in some cases leading to increased species richness, dispersal limitation may weaken this relationship. The species composition of these communities may be driven by stochastic processes rather than variation in host plant characteristics or differential predation by insectivorous birds.     

Phylogeny, niches, and relative abundance in natural communities

Community structure refers to the number of species in a community and the pattern of distribution of individuals among those species. We use a novel way of representing community structure to show that abundance within closely related pairs of co-occurring tree species in a highly diverse Mexican forest is more equitable than is abundance within more distantly related pairs. This observation is at odds with the fundamental assumption of neutral models of community structure, i.e., that species are interchangeable. The observed patterns suggest niche apportionment, in which interaction is focused pairwise between congeners but falls away from the phylogenetic structure above the genus level. Thus niche processes may significantly affect community structure through regulating relative abundance in a substantial proportion of species, which in turn potentially enhances community stability. One such mechanism of stable coexistence has already been shown to be active in this forest.     

Zooplankton biodiversity and lake trophic state: explanations invoking resource abundance and distribution

While empirical studies linking biodiversity to local environmental gradients have emphasized the importance of lake trophic status (related to primary productivity), theoretical studies have implicated resource spatial heterogeneity and resource relative ratios as mechanisms behind these biodiversity patterns. To test the feasibility of these mechanisms in natural aquatic systems, the biodiversity of crustacean zooplankton communities along gradients of total phosphorus (TP) as well as the vertical heterogeneity and relative abundance of their phytoplankton resources were assessed in 18 lakes in Quebec, Canada. Zooplankton community richness was regressed against TP, the spatial distribution of phytoplankton spectral groups, and the relative biomass of spectral groups. Since species richness does not adequately capture ecological function and life history of different taxa, features which are important for mechanistic theories, relationships between zooplankton functional diversity (FD) and resource conditions were examined. Zooplankton species richness showed the previously established tendency to a unimodal relationship with TP, but functional diversity declined linearly over the same gradient. Changes in zooplankton functional diversity could be attributed to changes in both the spatial distribution and type of phytoplankton resource. In the studied lakes, spatial heterogeneity of phytoplankton groups declined with TP, even while biomass of all groups increased. Zooplankton functional diversity was positively related to increased heterogeneity in cyanobacteria spatial distribution. However, a smaller amount of variation in functional diversity was also positively related to the ratio of biomass in diatoms/chrysophytes to cyanobacteria. In all observed relationships, a greater variation of functional diversity than species richness measures was explained by measured factors, suggesting that functional measures of zooplankton communities will benefit ecological research attempting to identify mechanisms behind environmental gradients affecting diversity.     

Spider, bee, and bird communities in cities are shaped by environmental control and high stochasticity

Spatially organized distribution patterns of species and communities are shaped by both autogenic processes (neutral mechanism theory) and exogenous processes (niche theory). In the latter, environmental variables that are themselves spatially organized induce spatial structure in the response variables. The relative importance of these processes has not yet been investigated in urban habitats. We compared the variance explained by purely spatial, spatially structured environmental, and purely environmental components for the community composition of spiders (Araneae), bees (Apidae), and birds (Aves) at 96 locations in three Swiss cities. Environmental variables (topography, climate, land cover, urban green management) were measured on four different radii around sampling points (< 10 m, 50 m, 250 m, 1000 m), while Moran's eigenvector maps (MEMs) acted as spatial variables. All three taxonomic groups showed weak spatial structure. Spider communities reacted to very fine-scaled environmental changes of lawn and meadow management and climate. Bird community composition was determined by woody plants as well as solar radiation at all radii, the scale of the influence varying among species. Bee communities were weakly explained by isolated variables only. Our results suggest that the anthropogenic structuring of urban areas has disrupted the spatial organization of environmental variables and inhibited the development of biotic spatial processes. The near absence of spatial structure may therefore be a feature typical of urban species assemblages, resulting in urban community composition mainly influenced by local environmental variables. Urban environments represent a close-knit mosaic of habitats that are regularly disturbed. Species communities in urban areas are far from equilibrium. Our analysis also suggests that urban communities need to be considered as being in constant change to adapt to disturbances and changes imposed by human activities.     

Species phylogenetic relatedness, priority effects, and ecosystem functioning

Species immigration history can structure ecological communities through priority effects, which are often mediated by competition. As competition tends to be stronger between species with more similar niches, we hypothesize that species phylogenetic relatedness, under niche conservatism, may be a reasonable surrogate of niche similarity between species, and thus influence the strength of priority effects. We tested this hypothesis using a laboratory microcosm experiment in which we established bacterial species pools with different levels of phylogenetic relatedness and manipulated the immigration history of species from each pool into microcosms. Our results showed that strong priority effects, and hence multiple community states, only emerged for the species pool with the greatest phylogenetic relatedness. Community assembly also resulted in a significant positive relationship between bacterial phylogenetic diversity and ecosystem functions. Interestingly, these results emerged despite a lack of phylogenetic conservatism for most of the bacterial functional traits considered. Our results highlight the utility of phylogenetic information for understanding the structure and functioning of ecological communities, even when phylogenetically conserved functional traits are not identified or measured.     

Regional-scale variation in the distribution and abundance of farming damselfishes on Australia’s Great Barrier Reef

Territorial damselfishes that manipulate (“farm”) the algae in their territories can have a marked effect on benthic community structure and may influence coral recovery following disturbances. Despite the numerical dominance of farming species on many reefs, the importance of their grazing activities is often overlooked, with most studies only examining their roles over restricted spatial and temporal scales. We used the results of field surveys covering 9.5° of latitude of the Great Barrier Reef to describe the distribution, abundance and temporal dynamics of farmer communities. Redundancy analysis revealed unique subregional assemblages of farming species that were shaped by the combined effects of shelf position and, to a lesser extent, by latitude. These spatial patterns were largely stable through time, except when major disturbances altered the benthic community. Such disturbances affected the functional guilds of farmers in different ways. Since different guilds of farmers modify benthic community structure and affect survival of juvenile corals in different ways, these results have important implications for coral recovery following disturbances.     

Currents connecting communities: nearshore community similarity and ocean circulation

Understanding the mechanisms that create spatial heterogeneity in species distributions is fundamental to ecology. For nearshore marine systems, most species have a pelagic larval stage where dispersal is strongly influenced by patterns of ocean circulation. Concomitantly, nearshore habitats and the local environment are also influenced by ocean circulation. Because of the shared dependence on the seascape, distinguishing the relative importance of the local environment from regional patterns of dispersal for community structure remains a challenge. Here, we quantify the "oceanographic distance" and "oceanographic asymmetry" between nearshore sites using ocean circulation modeling results. These novel metrics quantify spatial separation based on realistic patterns of ocean circulation, and we explore their explanatory power for intertidal and subtidal community similarity in the Southern California Bight. We find that these metrics show significant correspondence with patterns of community similarity and that their combined explanatory power exceeds that of the thermal structure of the domain. Our approach identifies the unique influence of ocean circulation on community structure and provides evidence for oceanographically mediated dispersal limitation in nearshore marine communities.     

Geographic structure of pollinator communities, reproductive assurance, and the evolution of self-pollination

Reproductive assurance is often invoked as an explanation for the evolution of self-fertilization in plants. However, key aspects of this hypothesis have received little empirical support. In this study, I use geographic surveys of pollinator communities along with functional studies of floral trait variation to examine the role of pollination ecology in mating system differentiation among populations and subspecies of the annual plant Clarkia xantiana. A greenhouse experiment involving 30 populations from throughout the species' range indicated that variation in two floral traits, herkogamy and protandry, was closely related to levels of autofertility and that trait variation was partitioned mainly among populations. Emasculation experiments in the field showed that autonomous selfing confers reproductive assurance by elevating fruit and seed production. Surveys of pollinator communities across the geographic range of the species revealed that bee pollinator abundance and community composition differed dramatically between populations of the outcrossing subspecies xantiana and the selfing subspecies parviflora despite their close proximity. Specialist bee pollinators of Clarkia were absent from selfing populations, but they were the most frequent visitors to outcrossing populations. Moreover, within the outcrossing subspecies xantiana, there was a close correspondence between specialist abundance and population differentiation in herkogamy, a key mating system trait. This spatial covariation arose, in part, because geographically peripheral populations had reduced herkogamy, higher autofertility, and lower pollinator abundance compared to central populations of xantiana. Finally, I detected strong spatial structure to bee communities both across the range of the species and within the outcrossing subspecies. In both cases, spatial structure was stronger for specialist bees compared to generalist bees, and pollinator communities varied in parallel with population variation in herkogamy. These results provide evidence that mating system differentiation parallels spatial variation in pollinator abundance and community composition at both broad and more restricted spatial scales, consistent with the hypothesis that pollinator abundance and reproductive assurance are important drivers of plant mating system evolution.     

Life history traits predict relative abundance in an assemblage of forest caterpillars

Species in a given trophic level occur in vastly unequal abundance, a pattern commonly documented but poorly explained for most taxa. Theoretical predictions of species density such as those arising from the metabolic theory of ecology hold well at large spatial and temporal scales but are not supported in many communities sampled at a relatively small scale. At these scales ecological factors may be more important than the inherent limits to energy use set by allometric scaling of mass. These factors include the amount of resources available, and the ability of individuals to convert these resources successfully into population growth. While previous studies have demonstrated the limits of macroecological theory in explaining local abundance, few studies have tested alternative generalized mechanisms determining abundance at the community scale. Using an assemblage of forest moth species found co-occurring as caterpillars on a single host plant species, we tested whether species abundance on that plant could be explained by mass allometry, intrinsic population growth, diet breadth, or some combination of these traits. We parameterized life history traits of the caterpillars in association with the host plant in both field and laboratory settings, so that the population growth estimate was specific to the plant on which abundance was measured. Using a generalized least-squares regression method incorporating phylogenetic relatedness, we found no relationship between abundance and mass but found that abundance was best explained by both intrinsic population growth rate and diet breadth. Species population growth potential was most affected by survivorship and larval development time on the host plant. Metabolic constraints may determine upper limits to local abundance levels for species, but local community abundance is strongly predicted by the potential for population increase and the resources available to that species in the environment.     

Can entropy maximization use functional traits to explain species abundances? A comprehensive evaluation

Entropy maximization (EM) is a method that can link functional traits and community composition by predicting relative abundances of each species in a community using limited trait information. We developed a complementary suite of tests to examine the strengths and limitations of EM and the community-aggregated traits (CATs; i.e., weighted averages) on which it depends that can be applied to virtually any plant community data set. We show that suites of CATs can be used to differentiate communities and that EM can address the classic problem of characterizing ecological niches by quantifying constraints (CATs) on complex trait relationships in local communities. EM outperformed null models and comparable regression models in communities with different levels of dominance, diversity, and trait similarity. EM predicted well the abundance of the dominant species that drive community-level traits; it typically identified rarer species as such, although it struggled to predict the abundances of the rarest species in some cases. Predictions were sensitive to choice of traits, were substantially improved by using informative priors based on null models, and were robust to variation in trait measurement due to intraspecific variability or measurement error. We demonstrate how similarity in species' traits confounds predictions and provide guidelines for applying EM.     

Multi-scale marine biodiversity patterns inferred efficiently from habitat image processing

Cost-effective proxies of biodiversity and species abundance, applicable across a range of spatial scales, are needed for setting conservation priorities and planning action. We outline a rapid, efficient, and low-cost measure of spectral signal from digital habitat images that, being an effective proxy for habitat complexity, correlates with species diversity and requires little image processing or interpretation. We validated this method for coral reefs of the Great Barrier Reef (GBR), Australia, across a range of spatial scales (1 m to 10 km), using digital photographs of benthic communities at the transect scale and high-resolution Landsat satellite images at the reef scale. We calculated an index of image-derived spatial heterogeneity, the mean information gain (MIG), for each scale and related it to univariate (species richness and total abundance summed across species) and multivariate (species abundance matrix) measures of fish community structure, using two techniques that account for the hierarchical structure of the data: hierarchical (mixed-effect) linear models and distance-based partial redundancy analysis. Over the length and breadth of the GBR, MIG alone explained up to 29% of deviance in fish species richness, 33% in total fish abundance, and 25% in fish community structure at multiple scales, thus demonstrating the possibility of easily and rapidly exploiting spatial information contained in digital images to complement existing methods for inferring diversity and abundance patterns among fish communities. Thus, the spectral signal of unprocessed remotely sensed images provides an efficient and low-cost way to optimize the design of surveys used in conservation planning. In data-sparse situations, this simple approach also offers a viable method for rapid assessment of potential local biodiversity, particularly where there is little local capacity in terms of skills or resources for mounting in-depth biodiversity surveys.     

Landscape of fear influences the relative importance of consumptive and nonconsumptive predator effects

Predators can initiate trophic cascades by consuming and/or scaring their prey. Although both forms of predator effect can increase the overall abundance of prey's resources, nonconsumptive effects may be more important to the spatial and temporal distribution of resources because predation risk often determines where and when prey choose to forage. Our experiment characterized temporal and spatial variation in the strength of consumptive and nonconsumptive predator effects in a rocky intertidal food chain consisting of the predatory green crab (Carcinus maenas), an intermediate consumer (the dogwhelk, Nucella lapillus), and barnacles (Semibalanus balanoides) as a resource. We tracked the survival of individual barnacles through time to map the strength of predator effects in experimental communities. These maps revealed striking spatiotemporal patterns in Nucella foraging behavior in response to each predator effect. However, only the nonconsumptive effect of green crabs produced strong spatial patterns in barnacle survivorship. Predation risk may play a pivotal role in determining the small-scale distribution patterns of this important rocky intertidal foundation species. We suggest that the effects of predation risk on individual foraging behavior may scale up to shape community structure and dynamics at a landscape level.     

The influence of spatial and size scale on phylogenetic relatedness in tropical forest communities

The relative importance of biotic, abiotic, and stochastic processes in structuring ecological communities continues to be a central focus in community ecology. In order to assess the role of phylogenetic relatedness on the nature of biodiversity we first quantified the degree of phylogenetic niche conservatism of several plant traits linked to plant form and function. Next we quantified the degree of phylogenetic relatedness across two fundamental scaling dimensions: plant size and neighborhood size. The results show that phylogenetic niche conservatism is likely widespread, indicating that closely related species are more functionally similar than distantly related species. Utilizing this information we show that three of five tropical forest dynamics plots (FDPs) exhibit similar scale-dependent patterns of phylogenetic structuring using only a spatial scaling axis. When spatial- and size-scaling axes were analyzed in concert, phylogenetic overdispersion of co-occurring species was most important at small spatial scales and in four of five FDPs for the largest size class. These results suggest that phylogenetic relatedness is increasingly important: (1) at small spatial scales, where phylogenetic overdispersion is more common, and (2) in large size classes, where phylogenetic overdispersion becomes more common throughout ontogeny. Collectively, our results highlight the critical spatial and size scales at which the degree of phylogenetic relatedness between constituent species influences the structuring of tropical forest diversity.     

The problem and promise of scale dependency in community phylogenetics

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.     

Determining patterns of variability in ecological communities: time lag analysis revisited

All ecological communities experience change over time. One method to quantify temporal variation in the patterns of relative abundance of communities is time lag analysis (TLA). It uses a distance-based approach to study temporal community dynamics by regressing community dissimilarity over increasing time lags (one-unit lags, two-unit lags, three-unit lags). Here, we suggest some modifications to the method and revaluate its potential for detecting patterns of community change. We apply Hellinger distance based TLA to artificial data simulating communities with different levels of directional and stochastic dynamics and analyse their effects on the slope and its statistical significance. We conclude that statistical significance of the TLA slope (obtained by a Monte Carlo permutation procedure) is a valid criterion to discriminate between (i) communities with directional change in species composition, regardless whether it is caused by directional abundance change of the species or by stochastic change according to a Markov process, and (ii) communities that are composed of species with population sizes oscillating around a constant mean or communities whose species abundances are governed by a white noise process. TLA slopes range between 0.02 and 0.25, depending on the proportions of species with different dynamics; higher proportions of species with constant means imply shallower slopes; and higher proportions of species with stochastic dynamics or directional change imply steeper slopes. These values are broadly in line with TLA slopes from real world data. Caution must be exercised when TLA is used for the comparison of community time series with different lengths since the slope depends on time series length and tends to decrease non-linearly with it.     

Disentangling the effects of heterogeneity, stochastic dynamics and sampling in a community of aquatic insects

A dynamic and heterogeneous species abundance model generating the lognormal species abundance distribution is fitted to time series of species data from an assemblage of stoneflies and mayflies (Plecoptera and Ephemeroptera) of an aquatic insect community collected over a period of 15 years. In each year except one, we analyze 5 parallel samples taken at the same time of the season giving information about the over-dispersion in the sampling relative to the Poisson distribution. Results are derived from a correlation analysis, where the correlation in the bivariate normal distribution of log abundance is used as measurement of similarity between communities. The analysis enables decomposition of the variance of the lognormal species abundance distribution into three components due to heterogeneity among species, stochastic dynamics driven by environmental noise, and over-dispersion in sampling, accounting for 62.9, 30.6 and 6.5% of the total variance, respectively. Corrected for sampling the heterogeneity and stochastic components accordingly account for 67.3 and 32.7% of the among species variance in log abundance. By using this method, it is possible to disentangle the effect of heterogeneity and stochastic dynamics by quantifying these components and correctly remove sampling effects on the observed species abundance distribution.     

Distribution and diversity of macrobenthic communities in the Jiangsu Reach of the Yangtze River北大核心CSCD

Macrobenthic communities are an important part of aquatic ecological system in the Yangtze River. Studies on macrobenthic community structure and diversity have important significance for development and protection of water resources in the Yangtze River. In this research, macrobenthic communities and their habitat in the Jiangsu Reach of the Yangtze River were investigated at 17 sites in May and September of 2013. Shannon-wiener diversity index was used to assess the diversity of macrobenthic communities. The results showed that there were 36 species at these 17 sites; the abundance and diversity of macrobenthic community were the highest in the Nanjing Reach and the Changzhou Reach, the lowest in the Nantong Reach of the Yangtze River. Nephthys sp., Grandidierella chaohuensis sp., Gammarus sp., Tubifex sp. and Limnodrilus hoffmeisteri were the dominant taxa in the Jiangsu Reach of the Yangtze River. Cluster analysis based on species abundance yielded four groups among the 17 sites. One-way analysis of similarity (ANOSIM) suggested significant differences in macrobenthic community structure among the four groups (P < 0.05). The results indicated that factors including aquatic plants, water flow velocity, sediment types and channels can influence the distribution and diversity of macrobenthic communities in the Jiangsu Reach of the Yangtze River.