Parametric scaling from species to growth-form diversity: an interesting analogy with multifractal functions

We propose a measure of divergence from species to life-form diversity aimed at summarizing the ecological similarity among different plant communities without losing information on traditional taxonomic diversity. First, species and life-form relative abundances within a given plant community are determined. Next, using Rényi's generalized entropy, the diversity profiles of the analyzed community are computed both from species and life-form relative abundances. Finally, the speed of decrease from species to life-form diversity is obtained by combining the outcome of both profiles. Interestingly, the proposed measure shows some formal analogies with multifractal functions developed in statistical physics for the analysis of spatial patterns. As an application for demonstration, a small data set from a plant community sampled in the archaeological site of Paestum (southern Italy) is used.     

Individual species–area relationships and spatial patterns of species diversity in a Great Basin,semi‐arid shrubland

Traditional biodiversity metrics operate at the level of a plant community but do not capture spatial variation in diversity from a ‘plant's‐eye view’ of a community. Recently‐developed statistics consider the spatial patterns of plants as well as the number and distribution of species in local plant neighborhoods to quantitatively assess multispecies spatial patterns from a ‘plant's‐eye view’. We used one such statistic, the individual species area relationship (ISAR), to assess spatial patterns of species diversity in a Great Basin (USA) semi‐arid shrubland through an analysis of a spatial dataset on shrub species and locations. In conjunction with appropriate null models, the ISAR blends species area relationships with second‐order spatial statistics to measure the expected species richness in local neighborhoods of variable size around the individuals of a focal species within a community. We found that, contrary to a previous analysis using more traditional methods, the community was well‐mixed with a typical shrub surrounded on average by 4.9 shrub neighbors of 2.1 species at a neighborhood scale of 1.0 m. We also found statistically significant fine‐scale variation in diversity patterns, such that neighborhoods of two species were more diverse than expected by a heterogeneous Poisson null model that accounted for larger‐scale habitat heterogeneity. However, this effect was caused by intraspecific aggregation of these species and was not due to positive interspecific association. Contrary to previous findings in other semi‐arid shrublands, our analysis suggests that the spatial pattern of the shrub community was not significantly structured by interspecific facilitation. This result supports growing evidence for balanced species patterns of adult plants in multispecies communities. Our approach may be used in other communities to describe complex multispecies spatial patterns, quantify species‐specific associations with diversity patterns, and to generate hypotheses regarding relationships between patterns and community‐structuring processes.     

Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales

Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.     

北京东灵山土壤动物多样性海拔格局的尺度推绎规律

识别群落内部各类群多样性格局的复杂性是生态学家面临的挑战,而尺度推绎规律是揭示复杂生态结构的有效途径之一。本研究利用多重分形的方法探索了不同海拔土壤动物多样性格局的尺度推绎规律,对比分析了凋落物层和土壤层之间多重分形谱的差异。结果表明: 与之前对植物群落的分析结果相似,土壤动物多样性尺度推绎规律同样具有幂律特征,如丰富度、Shannon多样性指数和Simpson多样性的倒数。凋落物层和土壤层中不同相对多度土壤动物的丰富度也具有幂律尺度推绎规律。凋落物层和土壤层中土壤动物多样性格局都具有多重分形特征,但凋落物层中多样性的分形结构比土壤层更均匀,且两层间优势类群与稀有类群的尺度推绎特征在多重分形谱上不同格局。幂律尺度推绎规律对于有着较高丰富度与多度的土壤动物同样存在,从而有助于揭示地下生物多样性的空间分布机制。     

Moving beyond abundance distributions: neutral theory and spatial patterns in a tropical forest

Assessing the relative importance of different processes that determine the spatial distribution of species and the dynamics in highly diverse plant communities remains a challenging question in ecology. Previous modelling approaches often focused on single aggregated forest diversity patterns that convey limited information on the underlying dynamic processes. Here, we use recent advances in inference for stochastic simulation models to evaluate the ability of a spatially explicit and spatially continuous neutral model to quantitatively predict six spatial and non-spatial patterns observed at the 50 ha tropical forest plot on Barro Colorado Island, Panama. The patterns capture different aspects of forest dynamics and biodiversity structure, such as annual mortality rate, species richness, species abundance distribution, beta-diversity and the species–area relationship (SAR). The model correctly predicted each pattern independently and up to five patterns simultaneously. However, the model was unable to match the SAR and beta-diversity simultaneously. Our study moves previous theory towards a dynamic spatial theory of biodiversity and demonstrates the value of spatial data to identify ecological processes. This opens up new avenues to evaluate the consequences of additional process for community assembly and dynamics.     

格氏栲自然保护区常绿阔叶林群落特征

在11000m²样地调查材料的基础上,分析了福建三明格氏栲自然保护区常绿阔叶林群落的种类组成、乔木种群的重要值、群落外貌、物种多样性、水平结构和垂直结构特征。该群落计有维管植物223种,隶属于80个科159属,其中单种属占总属数的80.5%,包括藤本在内的高位芽植物占总种数的85.2%。重要值高的乔木种群是格氏栲、木荷、米槠、马尾松、刮槠和山黄皮。主要乔木种群均服从聚集分布。群落垂直结构复杂,可分为乔木层、灌木层和草本层。生活型谱和物种多样性指数介于南亚热带季风常绿阔叶林和中亚热带常绿阔叶林之间。     

Fractal analysis of plant spatial patterns: a monitoring tool for vegetation transition shifts

Spatial heterogeneity, like species diversity, is an important ecosystem property. We examine the effects of land use on the diversity and spatial distribution of plants in five semi-arid communities of eastern Spain using non-linear methods to assess the spatialtemporal dynamics of plant populations. Specifically, we are interested in detecting long-term structural changes or drift in an ecosystem before it is too late to prevent irreversible degradation. Fractal analysis is used to characterize the complexity of plant spatial patterns and Information Theory indices are used to measure change in information flow with land use changes and soil substrate. We found that grazing favored diversity and heterogeneity of species distribution on the impoverished gypsum and saline substrate community, as opposed to the detrimental effect of grazing in the Alpha steppe community. Indeed, old-field succession after 30 years of abandonment showed a recovery of species diversity but not the spatial structure of the vegetation. Further, Information Fractal Dimension, representing the unpredictability of plant spatial patterns in the landscape, increased as we moved from a highly diverse to a less diverse community, revealing the change to a more scattered and homogeneous spatial plant distribution. The Information Fractal Dimension is a good estimator of ecosystem disturbance, independent of scale, and thus can be used to monitor ecosystem dynamics.     

Comparison of Rhizosphere Bacterial Communities in Arabidopsis thaliana Mutants for Systemic Acquired Resistance

Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a β-glucoronidase (GUS) reporter construct driven by the β-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon–Weiner, and Simpson’s diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages.     

Multifractal spatial patterns and diversity in an ecological succession

We analyzed the relationship between biodiversity and spatial biomass heterogeneity along an ecological succession developed in the laboratory. Periphyton (attached microalgae) biomass spatial patterns at several successional stages were obtained using digital image analysis and at the same time we estimated the species composition and abundance. We show that the spatial pattern was self-similar and as the community developed in an homogeneous environment the pattern is self-organized. To characterize it we estimated the multifractal spectrum of generalized dimensions D(q). Using D(q) we analyze the existence of cycles of heterogeneity during succession and the use of the information dimension D(1) as an index of successional stage. We did not find cycles but the values of D(1) showed an increasing trend as the succession developed and the biomass was higher. D(1) was also negatively correlated with Shannon's diversity. Several studies have found this relationship in different ecosystems but here we prove that the community self-organizes and generates its own spatial heterogeneity influencing diversity. If this is confirmed with more experimental and theoretical evidence D(1) could be used as an index, easily calculated from remote sensing data, to detect high or low diversity areas.     

Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar

Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.     

A conceptual framework for the spatial analysis of functional trait diversity

Functional trait diversity is a popular tool in modern ecology, mainly used to infer assembly processes and ecosystem functioning. Patterns of functional trait diversity are shaped by ecological processes such as environmental filtering, species interactions and dispersal that are inherently spatial, and different processes may operate at different spatial scales. Adding a spatial dimension to the analysis of functional trait diversity may thus increase our ability to infer community assembly processes and to predict change in assembly processes following disturbance or land‐use change. Richness, evenness and divergence of functional traits are commonly used indices of functional trait diversity that are known to respond differently to large‐scale filters related to environmental heterogeneity and dispersal and fine‐scale filters related to species interactions (competition). Recent developments in spatial statistics make it possible to separately quantify large‐scale patterns (variation in local means) and fine‐scale patterns (variation around local means) by decomposing overall spatial autocorrelation quantified by Moran's coefficient into its positive and negative components using Moran eigenvector maps (MEM). We thus propose to identify the spatial signature of multiple ecological processes that are potentially acting at different spatial scales by contrasting positive and negative components of spatial autocorrelation for each of the three indices of functional trait diversity. We illustrate this approach with a case study from riparian plant communities, where we test the effects of disturbance on spatial patterns of functional trait diversity. The fine‐scale pattern of all three indices was increased in the disturbed versus control habitat, suggesting an increase in local scale competition and an overall increase in unexplained variance in the post‐disturbance versus control community. Further research using simulation modeling should focus on establishing the proposed link between community assembly rules and spatial patterns of functional trait diversity to maximize our ability to infer multiple processes from spatial community structure.     

Altitude effects on spatial components of vascular plant diversity in a subarctic mountain tundra

Environmental gradients are caused by gradual changes in abiotic factors, which affect species abundances and distributions, and are important for the spatial distribution of biodiversity. One prominent environmental gradient is the altitude gradient. Understanding ecological processes associated with altitude gradients may help us to understand the possible effects climate change could have on species communities. We quantified vegetation cover, species richness, species evenness, beta diversity, and spatial patterns of community structure of vascular plants along altitude gradients in a subarctic mountain tundra in northern Sweden. Vascular plant cover and plant species richness showed unimodal relationships with altitude. However, species evenness did not change with altitude, suggesting that no individual species became dominant when species richness declined. Beta diversity also showed a unimodal relationship with altitude, but only for an intermediate spatial scale of 1 km. A lack of relationships with altitude for either patch or landscape scales suggests that any altitude effects on plant spatial heterogeneity occurred on scales larger than individual patches but were not effective across the whole landscape. We observed both nested and modular patterns of community structures, but only the modular patterns corresponded with altitude. Our observations point to biotic regulations of plant communities at high altitudes, but we found both scale dependencies and inconsistent magnitude of the effects of altitude on different diversity components. We urge for further studies evaluating how different factors influence plant communities in high altitude and high latitude environments, as well as studies identifying scale and context dependencies in any such influences.     

Spatial scale dependence of the species diversityin Tianmu Mountain and its relationship with spatial patterns by using multifractal analysis

This study took the Tianmu Mountain National Natural Preservation Area in western Zhejiang Province as an example 1) to quantify the species diversity with selected species indices including Shannon-Wiener index (H), Margalef index (K) and Evenness index (E) at different spatial scales, 2) to analyze the spatial distribution patterns of the species diversity by multifractal parameters such as the singularity index α, its fractal dimension f(α), the f(α)–α spectrum range (SR) and its symmetry (Dist) using the multifractal theory, and 3) to determine their relationships. Results of nonlinear regression analysis with power functions showed that increasing spatial scale resulted in increasing H but decreasing E and K, indicating that the scale dependence of species diversity existed. By using the multifractal method, it was indicated that species spatial distribution had multifractal features. Moreover, strong linear relationships of the diversity indices H, E and K with α_min and clear nonlinear associations of the diversity indices H, E and K with power functions for SR and Dist were found. Since interactions of the species diversity and the spatial characteristics are very complex, the above mentioned relationships need further validation along with precise explanations of any correlations among their ecological processes.     

Spatial patterns of plant diversity below-ground as revealed by DNA barcoding

Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.     

Biodiversity–productivity relationship in ponds: Community and metacommunity patterns along time and environmental gradients

Primary production correlates with diversity in various ways. These patterns may result from the interaction of various mechanisms related to the environmental context and the spatial and temporal scale of analysis. However, empirical evidence on diversity‐productivity patterns typically considers single temporal and spatial scales, and does not include the effect of environmental variables. In a metacommunity of macrophytes in ephemeral ponds, we analysed the diversity‐productivity relationship patterns in the field, the importance of the environmental variables of pond size and heterogeneity on such relationship, and the variation of these patterns at local (community level) and landscape scales (metacommunity level) across 52 ponds on twelve occasions, over five years (2005–2009). Combining all sampling dates, there were 377 ponds and 1954 sample‐unit observations. Vegetation biomass was used as a proxy for productivity, and biodiversity was represented by species richness, evenness, and their interaction. Environmental variables comprised pond area, depth and internal heterogeneity. Productivity and species richness were not directly related at the metacommunity level, and were positively related at the community level. Taking environmental variables into account revealed positive species richness‐productivity relationships at the metacommunity level and positive quadratic relationships at the community level. Productivity showed both positive and negative linear and nonlinear relationships with the size and heterogeneity of ponds. We found a weak relationship between productivity and evenness. The identity of variables associated with productivity changed between spatial scales and through time. The pattern of relationships between productivity and diversity depends on spatial scale and environmental context, and changes idiosyncratically through time within the same ecosystem. Thus, the diversity‐productivity relationship is not only a property of the study system, but also a consequence of environmental variations and the temporal and spatial scale of analysis.     

Phylogenetic and functional diversity area relationships in two temperate forests

Phylogenetic diversity (PD, the diversity of lineages) and functional diversity (FD, the diversity of functional traits or groups in a biological community) reflect important yet poorly understood attributes of species assemblages. Until recently, few studies have examined the spatial variation of PD and FD in natural communities. Yet the relationships between PD and FD and area (termed PDAR and FDAR), like the analogous species–area relationship (SAR), have received less attention and may provide insights into the mechanisms that shape the composition and dynamics of ecological communities. In this study, we used four spatial point process models to evaluate the likely roles of the random placement of species, habitat filtering, dispersal limitation, and the combined effects of habitat filtering and dispersal limitation in producing observed PDARs and FDARs in two large, fully mapped temperate forest research plots in northeast China and in north‐central USA. We found that the dispersal limitation hypothesis provided a good approximation of the accumulation of PD and FD with increasing area, as it did for the species area curves. PDAR and FDAR patterns were highly correlated with the SAR. We interpret this as evidence that species interactions, which are often influenced by phylogenetic and functional similarity, may be relatively unimportant in structuring temperate forest tree assemblages at this scale. However, the scale‐dependent departures of the PDAR and FDAR that emerged for the dispersal limitation hypothesis agree with operation of competitive exclusion at small scales and habitat filtering at larger scales. Our analysis illustrates how emergent community patterns in fully mapped temperate forest plots can be influenced by multiple underlying processes at different spatial scales.     

DNA reassociation kinetics and diversity indices: richness is not rich enough

DNA reassociation kinetics, also known as Cot curves, were recently used by Gans and co-workers to estimate the number of bacterial species present in soil samples. By reanalysing the mathematical model we show that rather than the number of species, Simpson and Shannon diversity indices are encoded in the experimental data. Our main tool to establish this result are the so-called Rényi diversities, closely related to Hill numbers, illustrating the power of these concepts in interpreting ecological data. We argue that the huge diversity encountered in microbial ecology can be quantified more informatively by diversity indices than by number of species.     

Spatio-temporal Processes in a Calcareous Grassland

Abstract The herbaceous plant communities occurring on nutrient-poor calcareous soils of north-western Europe are typically rich in species, with as many as 30–40 species m^-2. It is an open question as to what dynamic properties allow this diversity. We review evidence that we have collected on the spatial and temporal processes operating in a calcareous grassland community in England to address this issue. Our data indicate spatial aggregation of individuals within species consistent with the modular growth of the species concerned, but there is little evidence to suggest spatial structure generated by interactions between species, and we have been unable to separate most species tested into different niches. The development of spatial structure of the community through time is also consistent with dynamics that depend principally on the modular growth patterns of the different species. We suggest that there is a nonlinearity in the per capita rate of increase with the property that the community is no more than weakly dependent on densities of the species under natural conditions. The dynamic of the community is then driven more by forces external to the community than by density-dependent effects within the community.     

天目山物种多样性尺度依赖及其与空间格局关系的多重分形

以浙江省天目山国家级自然保护区为例,采用多尺度分析思想,利用多重分形分析方法,研究了不同尺度下物种多样性的变化、空间分布格局以及多样性与空间格局之间的关系。研究主要得到3方面的结论：（1）物种多样性具有尺度依赖性,随着空间尺度的增大,Shannon-Wiener多样性指数Ⅳ增大,Margalef多样性指数足和均匀度指数E减小;（2）多重分形参数αmin。多重分形谱的变化范围SR等能够定量反映物种的空间分布特征,空间大尺度越大,物种越聚集,空间分布越不均匀;（3）物种多样性与空间格局存在线性或幂函数关系。研究表明多重分形分析定量描述物种空间格局是有效性的,多重分形参数与生物多样性之间的定量关系为研究物种空间格局、生态属性与尺度之间的关系奠定了基础。因此,分形结合传统方法,在生物多样性方面的研究将有很大的潜在价值。     

From species distributions to meta‐communities

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta‐community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine‐resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.