Community‐level spatial structure supports a model of stochastic geometry in species‐rich shrublands

In some ecosystems a small suite of species can determine community‐level patterns of species richness by acting as either ‘accumulators’ or ‘repellers’; that is, the richness of the immediate neighbourhood of such species departs from that expected on the basis of a given null model. Using the individual species‐area approach, we evaluated community‐level spatial pattern in four species‐rich shrublands (two 40 × 40 m and two 30 × 30 m plots) by assessing the frequency of accumulator and repeller species and whether any such species were associated with specific life‐history characteristics. Few species departed from the expectations of the null spatial model that we used, although, at three of the four sites, accumulators were more common than repellers. Departures from the null model we assessed were most prevalent within just 1 m of focal individuals and were not consistently associated with specific life‐history traits. Model‐based clustering suggests that there are distinct sub‐communities in each of the four communities, but while internally spatially cohesive, these sub‐communities intermingle and their membership is not predictable from the life‐history traits of their constituent species. Comparable analyses in other species‐rich systems have also detected a similar absence of spatial interactions. The disturbance regime in the shrubland communities we consider is markedly different from those in the forest ecosystems where previous studies have been concentrated (recurrent fire versus infrequent gap‐phase dynamics) and resources are more limiting. Thus, our results provide further support for the generality of a model of stochastic geometry, likely underpinned by stochastic dilution effects, in species‐rich plant communities.     

The roles of stochasticity and biotic interactions in the spatial patterning of plant species in alpine communities

Questions

Plant community composition can be influenced by multiple biotic, abiotic, and stochastic factors acting on the local species pool to determine their establishment success and abundance and subsequently the diversity of the community. We asked if the influences of biotic interactions on the composition of plant species in communities, as indicated by patterns of plant species spatial associations (independent, positive or negative), vary across a productivity gradient within a single ecosystem type. Do dominant species of communities show spatial patterning suggestive of competitive interactions with interspecific neighbors? Do species that span multiple community types exhibit the same heterospecific interactions with neighbours in each community?

Location

Three alpine communities in the southern Rocky Mountains.

Methods

We measured the occurrence of species in a 1‐cm spatial grid within 2 m × 2 m plots to determine the spatial patterns of species pairs in the three communities. A null model of independent species spatial arrangements was used to determine whether species pairs were positively, negatively or independently associated, and how these patterns differed among the communities across the gradient of resource supply and environmental stress.

Results

Positive associations, indicative of facilitation between species, were most common in the most resource‐poor and least productive community. However negative associations, suggestive of competitive interactions among species, were not more common in the two more resource‐rich, productive communities. The dominant species of these communities did exhibit higher negative than positive associations with neighbours relative to positive patterning. Independent interspecific patterning was equally common relative to positive and negative patterns in all communities. Species that previously were shown to either facilitate other species or compete with neighbours exhibited spatial patterning consistent with the earlier experimental work.

Conclusions

A large number of species exhibit a lack of net biotic interactions, and stochastic factors appear to be as important as competition and facilitation in shaping the structure of the three alpine plant communities we studied.

     

Nearest-neighbour interactions in species-rich shrublands: the roles of abundance, spatial patterns and resources

We explored pairwise nearest‐neighbour interactions in four species‐rich shrubland plant communities, asking the question: how often is an individual of species j the nearest‐neighbour of species i? In the observed data and null models, less than 35% of the maximum possible number of nearest‐neighbour species pairs was present, and at three of the four sites the number of observed nearest‐neighbour pairs were significantly less than those occurring in simulated null communities. Many of the missing pairs included woody shrubs whose absence might be interpreted as evidence of site‐specific competition between larger growth forms for soil resources or space. Less than 5% of the pairs of species that occurred did so at frequencies different from that expected under random mixing, and many of these pairs were conspecific. Of the heterospecific pairs whose frequency differed significantly from random mixing there was a weak bias towards pairs occurring at higher rather than lower frequencies than expected. There was no evidence for asymmetry (interaction of species j with species i but not the reverse) in the frequency of species pairs. Nearest‐neighbour relationships are species‐specific rather than between plant functional types. The four sites form a soil nutrient and water availability gradient, and, according to the stress gradient hypothesis, positive species interactions should be most prevalent at the most stressful sites. However, we found the opposite: the site with the highest availability of resources had both proportionally the most heterospecific pairs, and the most conspecific and heterospecific species pairs with frequencies departing significantly from that expected under random mixing.     

Patterns of species associations in woody plants in forest communities of Putuoshan Island,Zhejiang, China

Aims Interspecific associations can reflect how species are assembled into communities. The objectives of this study were to examine the patterns of woody species co-occurrence and to determine how species’ abundance would affect species associations. Methods Data from a total of 23 plots were used to test the interspecific associations of 93 woody plant species in forest communities of Putuoshan Island in Zhejiang Province. We compared the observed species associations with the expected patterns at random, and correlated interspecific association intensities with co-dominance propensity of species pairs. Important findings Species distribution co-varied among plots at the spatial scale of either 10 m × 10 m or 20 m × 20 m, but the majority of the 4 278 species pairs were not significantly associated. Interspecific association intensities were positively correlated with co-dominance propensity of species pairs, indicating that species abundance is a key factor affecting the interspecific co-occurrence. The observed values of variance ratio and the proportion of significantly associated species pairs consistently fell outside of the 2.5th-97.5th percentiles of random expectations (i.e. randomly permuting species across plots), suggesting that deterministic processes also play a role in species associations on the Putuoshan Island. We conclude that the pattern of woody species co-occurrence on Putuoshan Island are structured by both niche and stochastic processes.     

Quantifying the role of deterministic assembly and stochastic drift in a natural community of Arctic mosses

The interpretation of natural plant communities frequently invokes species‐sorting controlled by niche differences along spatial environmental gradients. This process of niche structuring can be explained by reference to functional traits, which provide a mechanistic explanation for community structure. In contrast, models explaining species coexistence obviate the limiting effect of niche difference, by invoking processes which cause species‐level drift, e.g. demographic stochasticity. This paper investigates a simple habitat with strong gradients (moss communities in a patterned arctic wetland) to identify signature‐patterns under‐pinning the relative importance of deterministic assembly and stochastic drift in a natural community. First, ordination analysis was used to confirm community composition structured by a range of nine carefully selected functional traits. Second, to determine whether traits explaining community composition might also explain species richness, local species richness (sR) was compared to (1) observed trait diversity and (2) expected trait diversity based on permutation tests, which are used to simulate null community assembly for different values of sR. Traits explaining species composition, consistent with deterministic niche structuring, do not appear to maintain sR. This surprising result was explained by decomposing the community into individual pair‐wise comparisons, i.e. species niche‐differences and association (χ²). Results support deterministic processes via the sorting of species with similar and contrasting niches, at opposite ends of a composite environmental gradient. Nevertheless, stochastic drift is apparent in the random structure of a majority of pair‐wise associations; in addition, a species’ abundance was in general not related to environmental distance from response‐optima. We suggest therefore that spatial pattern in the moss community is a balance between deterministic forces with respect to species traits and controlling environmental gradients, and stochastic drift, which weakens this deterministic structure.     

Testing the independent species' arrangement assertion made by theories of stochastic geometry of biodiversity

The assertion that the spatial location of different species is independent of each other is fundamental in major ecological theories such as neutral theory that describes a stochastic geometry of biodiversity. However, this assertion has rarely been tested. Here we use techniques of spatial point pattern analysis to conduct a comprehensive test of the independence assertion by analysing data from three large forest plots with different species richness: a species-rich tropical forest at Barro Colorado Island (Panama), a tropical forest in Sinharaja (Sri Lanka), and a temperate forest in Changbaishan (China). We hypothesize that stochastic dilution effects owing to increasing species richness overpower signals of species associations, thereby yielding approximate species independence. Indeed, the proportion of species pairs showing: (i) no significant interspecific association increased with species richness, (ii) segregation decreased with species richness, and (iii) small-scale interspecific interaction decreased with species richness. This suggests that independence may indeed be a good approximation in the limit of very species-rich communities. Our findings are a step towards a better understanding of factors governing species-rich communities and we propose a hypothesis to explain why species placement in species-rich communities approximates independence.     

Shared environmental responses drive co‐occurrence patterns in river bird communities

Positive or negative patterns of co‐occurrence might imply an influence of biotic interactions on community structure. However, species may co‐occur simply because of shared environmental responses. Here, we apply two complementary modelling methodologies – a probabilistic model of significant pairwise associations and a hierarchical multivariate probit regression model – to 1) attribute co‐occurrence patterns in 100 river bird communities to either shared environmental responses or to other ecological mechanisms such as interaction with heterospecifics, and 2) examine the strength of evidence for four alternative models of community structure. Species co‐occurred more often than would be expected by random community assembly and the species composition of bird communities was highly structured. Co‐occurrence patterns were primarily explained by shared environmental responses; species’ responses to the environmental variables were highly divergent, with both strong positive and negative environmental correlations occurring. We found limited evidence for behaviour‐driven assemblage patterns in bird communities at a large spatial scale, although statistically significant positive associations amongst some species suggested the operation of facilitative mechanisms such as heterospecific attraction. This lends support to an environmental filtering model of community assembly as being the principle mechanism shaping river bird community structure. Consequently, species interactions may be reduced to an ancillary role in some avifaunal communities, meaning if shared environmental responses are not quantified studies of co‐occurrence may overestimate the role of species interactions in shaping community structure.     

Spatial patterns of species and plant traits in response to 20 years of grazing exclusion in subalpine grassland communities

Question: Does long‐term grazing exclusion affect spatial patterns of canopy height, plant species and traits in subalpine grassland communities? Are spatial patterns of species and traits similarly affected by grazing exclusion? Are changes in spatial patterns of species associated with changes in species abundances? Location: Subalpine grasslands, Vercors and Oisans Mountains, Alps (France). Methods: Spatial sampling of vegetation and measurements of plant traits were carried out within nine pairs of grazed and ungrazed 10 m × 10‐m plots in three species‐rich communities with different productivities. We estimated within‐plot spatial patterns of canopy height, species and aggregated trait values by measuring the extent (or patch size) and intensity of spatial dependence with Moran's I. Abundance‐weighted averages for species patch size and intensity of spatial dependence were calculated across all species per plot and across species per life form. Such measures derived from analysis of spatial dependence were considered spatial traits. Results: Response of spatial patterns to grazing exclusion was only detected in patch size, whereas intensity of spatial dependence was not affected. Changes in spatial patterns were community‐dependent because spatial traits based on patch size of canopy height and species increased following grazing exclusion only in the less productive community. Unexpectedly, changes in spatial patterns of species did not support changes in spatial patterns of trait values. Abundances and patch sizes of several life forms were significantly affected by grazing exclusion. However, at the scale investigated, changes in abundance of life forms did not correspond to changes in their spatial patterns and vice versa. Conclusion: In species‐rich communities, grazing alters spatial spread of species (i.e. patch size) rather than intra‐specific aggregation (i.e. intensity of spatial dependence). Results revealed possible mechanisms of species spatial reorganisation that are independent of abundance variation. Therefore, it is important to consider changes in spatial patterns in addition to changes in mean values of vegetation features when assessing impacts of grazing management.     

Spatial patterns and associations of four species in an old-growth temperate forest

The spatial pattern of a tree species is an important characteristic of plant communities, providing critical information to explain species coexistence. The spatial distribution and association of four different successional species were analyzed among different life-history stages in an old-temperate forest. Significant aggregation patterns were found, and the degree of aggregation decreased with the scales and life-history stages. Significant interspecific spatial associations were detected. In comparing the relationships among the different life-history stages, positive associations were found at small scales in all of the juvenile species pairs. In the adult stage, negative associations were detected in coniferous vs. deciduous species pairs, while the deciduous species pairs, which have identical resource requirements, showed a positive association in this study. The coniferous species pairs showed a positive association at small scales. We infer that seed dispersal, competitive ability, or the requirement for specific topographic and light environments may contribute to the coexistence of these species.     

Accounting for spatial autocorrelation in null models of tree species association

A commonly used null model for species association among forest trees is a well‐mixed community (WMC). A WMC represents a non‐spatial, or spatially implicit, model, in which species form nearest‐neighbor pairs at a rate equal to the product of their community proportions. WMC models assume that the outcome of random dispersal and demographic processes is complete spatial randomness (CSR) in the species’ spatial distributions. Yet, stochastic dispersal processes often lead to spatial autocorrelation (SAC) in tree species densities, giving rise to clustering, segregation, and other nonrandom patterns. Although methods exist to account for SAC in spatially‐explicit models, its impact on non‐spatial models often remains unaccounted for. To investigate the potential for SAC to bias tests based upon non‐spatial models, we developed a spatially‐heterogeneous (SH) modelling approach that incorporates measured levels of SAC. Using the mapped locations of individuals in a tropical tree community, we tested the hypothesis that the identity of nearest‐neighbors represents a random draw from neighborhood species pools. Correlograms of Moran's I confirmed that, for 50 of 51 dominant species, stem density was significantly autocorrelated over distances ranging from 50 to 200 m. The observed patterns of SAC were consistent with dispersal limitation, with most species occurring in distinct patches. For nearly all of the 106 species in the community, the frequency of pairwise association was statistically indistinguishable from that projected by the null models. However, model comparisons revealed that non‐spatial models more strongly underestimated observed species‐pair frequencies, particularly for conspecific pairs. Overall, the CSR models projected more significant facilitative interactions than did SH models, yielding a more liberal test of niche differences. Our results underscore the importance of accounting for stochastic spatial processes in tests of association, regardless of whether spatial or non‐spatial models are employed.     

伏牛山自然保护区森林生态系统草本植物功能群的分类

伏牛山国家级自然保护区是中国东部森林样带中的亚热带和暖温带的结合点,随着环境梯度(海拔)的变化,林下植物优势种变化明显.草本植物对环境的反应较为敏感,能较好的反映出植被与环境的动态关系.采用群落学调查方法,对伏牛山南北坡的植被进行调查.以X2检验为基础,结合联结系数AC和共同出现百分率PC来测定草本层优势种间的联结性,根据优势种间的联系性及其在海拔梯度上的变化异同,以优势种为主体划分伏牛山自然保护区林下草本植物功能群.研究结果表明,以优势种为主体对森林生态系统草本植物进行功能群划分可行性高,有较强的代表性.对草本优势种共划分了7组植物功能群:Ⅰ"伴人型",Ⅱ"高山型",Ⅲ"阴湿型",Ⅳ"耐旱型",Ⅴ"林隙型",Ⅵ"基础型",Ⅶ"原始型".每一组都有其特定的分布区域和形态特征,较好了反应出环境与植被的动态关系,为今后森林生态系统研究和植物功能群划分寻找新的思路.     

Nonrandom co-occurrence patterns of rainforest chameleons

Null‐model analysis of co‐occurrence patterns is a powerful tool to identify ‘structure’ in community ecology data sets. We evaluated the community structure of chameleons in rainforest regions of Nigeria and Cameroon using available data in the literature, including peer‐reviewed articles and unpublished environmental reports to industries. We performed Monte Carlo simulations (5000 iterations, using the sequential swap algorithm) under several model assumptions to derive co‐occurrence patterns among species. Food and spatial (habitat) segregation patterns in both lowland rainforest and montane forest were investigated. We subjected four indices of co‐occurrence patterns (C‐ratio, number of checkerboard species pairs, number of species combinations, and V‐score) to randomization procedures. Overall, the chameleon communities do not show random organization, but instead exhibit precise deterministic patterns. In lowland rainforest, chameleon communities are assembled deterministically along the food niche resource axis, but not along the habitat niche resource axis. The opposite holds for chameleon communities in montane rainforest. We predict that these patterns can be generalized to other regions of tropical Africa, thus helping to determine the general structure of chameleon communities in tropical African forests.     

Assembly mechanisms shaping tropical litter ant communities

Community ecology seeks to unravel the mechanisms that allow species to coexist in space. Some of the contending mechanisms may generate tractable signatures in the amount of trait and phylogenetic dispersion among co‐existing species. When a community presents a pattern with reduced trait or phylogenetic dispersion, mechanisms based on ecological filters are brought into consideration. On the other hand, limiting similarity mechanisms such as competitive exclusion are proposed when communities present patterns of trait or phylogenetic even‐dispersion. The strength of these mechanisms likely varies with the spatial scale of an observed sample. I surveyed species‐rich tropical litter ant communities in a spatially nested design that allowed me to explore the spatial scales, fine (0.25 m²), intermediate (9 m²), and broad (361 m²) at which these mechanisms act. I then assessed the relationship between observed ant communities and potential species pools ranging in size, from plot, site, and island‐wide areas. Patterns of phylogenetic dispersion within ant communities suggested that ant communities were composed of species that were more closely related than expected by a random sampling of phylogenetic pools. The magnitude of phylogenetic ‘clustering’ increased with the size of the species pool but was similar among communities assembled from different spatial scales. Patterns of dispersion of one ecological trait (i.e. body size) within ant communities also showed clustering of body sizes, and most communities were composed of ant species that were smaller than expected by a random sampling of trait pools. Trait clustering increased with the size of the species pool but decreased at broad spatial scales. Together, these results suggest that ecological filters, not interspecific interactions, are structuring tropical ant communities, favoring clades with small worker sizes. The larger dependency on the size of regional pools than on the spatial scale suggests that environmental heterogeneity is greater among than within the study sites.     

Correcting for bias in distribution modelling for rare species using citizen science data

Aim

To improve the accuracy of inferences on habitat associations and distribution patterns of rare species by combining machine‐learning, spatial filtering and resampling to address class imbalance and spatial bias of large volumes of citizen science data.

Innovation

Modelling rare species’ distributions is a pressing challenge for conservation and applied research. Often, a large number of surveys are required before enough detections occur to model distributions of rare species accurately, resulting in a data set with a high proportion of non‐detections (i.e. class imbalance). Citizen science data can provide a cost‐effective source of surveys but likely suffer from class imbalance. Citizen science data also suffer from spatial bias, likely from preferential sampling. To correct for class imbalance and spatial bias, we used spatial filtering to under‐sample the majority class (non‐detection) while maintaining all of the limited information from the minority class (detection). We investigated the use of spatial under‐sampling with randomForest models and compared it to common approaches used for imbalanced data, the synthetic minority oversampling technique (SMOTE), weighted random forest and balanced random forest models. Model accuracy was assessed using kappa, Brier score and AUC. We demonstrate the method by evaluating habitat associations and seasonal distribution patterns using citizen science data for a rare species, the tricoloured blackbird (Agelaius tricolor).

Main Conclusions

Spatial under‐sampling increased the accuracy of each model and outperformed the approach typically used to direct under‐sampling in the SMOTE algorithm. Our approach is the first to characterize winter distribution and movement of tricoloured blackbirds. Our results show that tricoloured blackbirds are positively associated with grassland, pasture and wetland habitats, and negatively associated with high elevations or evergreen forests during both winter and breeding seasons. The seasonal differences in distribution indicate that individuals move to the coast during the winter, as suggested by historical accounts.

     

Environmental heterogeneity among lakes promotes hyper β‐diversity across phytoplankton communities

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Community structure and positive interactions in constraining environments

Spatial patterns in plant communities are thought to be controlled by the interplay of species interactions and environmental constraints. To evaluate the role of plant–plant interactions in shaping these communities we quantified species co-occurrence and interaction in seven environmentally distinct communities. These included four different semiarid habitats in southeast Spain, one alpine system in the Sierra Nevada range (Spain), and two sites in Venezuela, a secondary savanna near Caracas (Altos de Pipe), and a sclerophyllous shrubland in the Gran Sabana plateau. We expected that facilitation would be stronger at sites with more spatial associations. The four semiarid sites in Spain and the shrubland in Gran Sabana showed a high degree of positive species associations. Of the other two communities, one showed both positive and negative associations while negative ones predominated in Altos de Pipe. The direct experimental measure of neighbors' effect showed that positive interactions among species prevailed in communities where positive species associations dominated. The appearance of benefactor species in patches increased species richness compared with the surrounding inter-shrub spaces. Our results provide a link between spatial patterns and species interactions, where aggregation points to positive interactions and segregation to competitive or interference effects. Facilitation appears as a relevant process shaping communities under environmental constraints.     

Anthropogenic modification disrupts species co‐occurrence in stream invertebrates

The question of whether species co‐occurrence is random or deterministic has received considerable attention, but little is known about how anthropogenic disturbance mediates the outcomes. By combining experiments, field surveys and analysis against null models, we tested the hypothesis that anthropogenic habitat modification disrupts species co‐occurrence in stream invertebrates across spatial scales. Whereas communities in unmodified conditions were structured deterministically with significant species segregation, catchment‐scale conversion to agriculture and sediment deposition at the patch‐ or micro‐habitat scale apparently randomized species co‐occurrences. This shift from non‐random to random was mostly independent of species richness, abundance and spatial scale. Data on community‐wide life‐history traits (body size, dispersal ability and predatory habits) and beta‐diversity indicated that anthropogenic modification disrupted community assembly by affecting biotic interactions and, to a lesser extent, altering habitat heterogeneity. These data illustrate that the balance between predictable and stochastic patterns in communities can reflect anthropogenic modifications that not only transcend scales but also change the relative forces that determine species coexistence. Research into the effects of habitat modification as a key to understanding global change should extend beyond species richness and composition to include species co‐occurrence, species interactions and any functional consequences.     

Oribatid mites reveal that competition for resources and trophic structure combine to regulate the assembly of diverse soil animal communities

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Species Associations in a Species-Rich Subtropical Forest Were Not Well-Explained by Stochastic Geometry of Biodiversity

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.