A multiple-site dissimilarity measure for species presence/absence data and its relationship with nestedness and turnover

Multiple-site dissimilarity may be caused by two opposite processes of meta-community organization, such as species nestedness and turnover. Therefore, discriminating among these contributions is necessary for linking multiple-site dissimilarity to ecosystem functioning. This paper introduces a measure of multiple-site dissimilarity or beta diversity for presence/absence data that is based on information on species absences from the species × sites matrix. It is also shown that the newly proposed dissimilarity index can be additively partitioned into species nestedness and turnover.     

Partitioning the turnover and nestedness components of beta diversity

Aim  Beta diversity (variation of the species composition of assemblages) may reflect two different phenomena, spatial species turnover and nestedness of assemblages, which result from two antithetic processes, namely species replacement and species loss, respectively. The aim of this paper is to provide a unified framework for the assessment of beta diversity, disentangling the contribution of spatial turnover and nestedness to beta-diversity patterns.
Innovation  I derive an additive partitioning of beta diversity that provides the two separate components of spatial turnover and nestedness underlying the total amount of beta diversity. I propose two families of measures of beta diversity for pairwise and multiple-site situations. Each family comprises one measure accounting for all aspects of beta diversity, which is additively decomposed into two measures accounting for the pure spatial turnover and nestedness components, respectively. Finally, I provide a case study using European longhorn beetles to exemplify the relevance of disentangling spatial turnover and nestedness patterns.
Main conclusion  Assigning the different beta-diversity patterns to their respective biological phenomena is essential for analysing the causality of the processes underlying biodiversity. Thus, the differentiation of the spatial turnover and nestedness components of beta diversity is crucial for our understanding of central biogeographic, ecological and conservation issues.     

The island-mainland species turnover relationship

Many oceanic islands are notable for their high endemism, suggesting that islands may promote unique assembly processes. However, mainland assemblages sometimes harbour comparable levels of endemism, suggesting that island biotas may not be as unique as is often assumed. Here, we test the uniqueness of island biotic assembly by comparing the rate of species turnover among islands and the mainland, after accounting for distance decay and environmental gradients. We modelled species turnover as a function of geographical and environmental distance for mainland (M-M) communities of Anolis lizards and Terrarana frogs, two clades that have diversified extensively on Caribbean islands and the mainland Neotropics. We compared mainland-island (M-I) and island-island (I-I) species turnover with predictions of the M-M model. If island assembly is not unique, then the M-M model should successfully predict M-I and I-I turnover, given geographical and environmental distance. We found that M-I turnover and, to a lesser extent, I-I turnover were significantly higher than predicted for both clades. Thus, in the first quantitative comparison of mainland-island species turnover, we confirm the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts.     

Habitat heterogeneity drives bird species richness,nestedness and habitat selection by individual species in fluvial wetlands of the Paraná River,Argentina

We assessed the relationship between habitat heterogeneity and bird species richness and composition within wetlands of the floodplain of the Middle Paraná River, Argentina. Given the high habitat heterogeneity in these wetland systems, we sought to determine whether (i) there was a positive relationship between bird species richness and habitat heterogeneity; (ii) whether bird species richness was associated with certain types of individual habitat types; (iii) whether there was a pattern of species nestedness and turnover between sites as a function of habitat heterogeneity and composition, respectively; and (iv) whether individual species exhibited associations with habitat heterogeneity. Point counts were used to survey birds at 60 sites. We estimated the area of eight habitat types found within a 200‐m radius from the centre of each site and calculated number and Pielou's evenness of habitat types. These indices, together with area proportion of each habitat type, were used as explanatory factors of bird species richness in linear regression models. Habitat heterogeneity per se rather than area of individual habitat types was a more important predictor of species richness in these fluvial wetlands. Sites with more habitat types supported more bird species. Results showed that individual bird species were associated with different habitat types and, therefore, sites that contained more habitat types contained more species. Number of habitat types accounted for species nestedness between sites whereas composition of habitat types accounted for species turnover between sites. Results suggest that selection of heterogeneous sites by individual species could help explain the positive heterogeneity–species richness relationship. Our findings highlight the importance of habitat heterogeneity per se resulting from flood disturbances in maintaining bird richness in fluvial systems.     

Determining the relative roles of species replacement and species richness differences in generating beta‐diversity patterns

Aim To determine the relative contribution of species replacement and species richness differences to the emergence of beta‐diversity patterns. Innovation A novel method that disentangles all compositional differences (β_cc, overall beta diversity) in its two components, species replacement (β_‐3) and species richness differences (β_rich) is proposed. The performance of the method was studied with ternary plots, which allow visualization of the influence of the relative proportions of shared and unique species of two sites over each metric. The method was also tested in different hypothetical gradients and with real datasets. The novel method was compared with a previous proposal based on the partitioning of overall compositional differences (β_sor) in replacement (β_sim) and nestedness (β_nes). The linear response of β_cc contrasts with the curvilinear response of β_sor to linear gradients of dissimilarity. When two sites did not share any species, β_sim was always 1 and β_‐3 only reached 1 when the number of exclusive species of both sites was equal. β_‐3 remained constant along gradients of richness differences with constant replacement, while β_sim decreased. β_rich had a linear response to a linear gradient of richness differences with constant species replacement, whereas β_nes exhibited a hump‐shaped response. Moreover, β_sim > β_nes when clearly almost all species of one site were lost, whereas β_‐3 < β_rich in the same circumstances. Main conclusions The behaviour of the partition of β_cc into β_‐3 and β_rich is consistent with the variation of replacement and richness differences. The partitioning of β_sor into β_sim and β_nes overestimates the replacement component and underestimates richness differences. The novel methodology allows the discrimination of different causes of beta‐diversity patterns along latitudinal, biogeographic or ecological gradients, by estimating correctly the relative contributions of replacement and richness differences.     

The relationships between local and regional species richness and spatial turnover

Aim To determine the empirical relationships between species richness and spatial turnover in species composition across spatial scales. These have remained little explored despite the fact that such relationships are fundamental to understanding spatial diversity patterns. Location South‐east Scotland. Methods Defining local species richness simply as the total number of species at a finer resolution than regional species richness and spatial turnover as turnover in species identity between any two or more areas, we determined the empirical relationships between all three, and the influence of spatial scale upon them, using data on breeding bird distributions. We estimated spatial turnover using a measure independent of species richness gradients, a fundamental feature which has been neglected in theoretical studies. Results Local species richness and spatial turnover exhibited a negative relationship, which became stronger as larger neighbourhood sizes were considered in estimating the latter. Spatial turnover and regional species richness did not show any significant relationship, suggesting that spatial species replacement occurs independently of the size of the regional species pool. Local and regional species richness only showed the expected positive relationship when the size of the local scale was relatively large in relation to the regional scale. Conclusions Explanations for the relationships between spatial turnover and local and regional species richness can be found in the spatial patterns of species commonality, gain and loss between areas.     

高寒草甸种间性状差异和物种均匀度对物种多样性与功能多样性关系的影响

物种多样性(SD)与功能多样性(FD)之间存在多种关系,但由于生态系统功能主要由物种的功能属性决定,因而功能多样性对生态系统功能的影响大于物种多样性的影响。但在种间性状差异和物种均匀度这两个构成功能多样性的基本成分中,何者对功能多样性影响更大,并进而决定SD-FD关系尚不明确。通过在高寒矮嵩草(Kobresia humilis)草甸为期6a的刈割(留茬1 cm、3 cm及不刈割)和施肥(尿素7.5 g m~(-2)a~(-1)+磷酸二胺1.8 g m~(-2)a~(-1)、不施肥)控制实验,研究了种间性状差异(33个物种13个性状)和物种均匀度(所有物种)对物种多样性(所有物种)与功能多样性(33个物种13个性状)之间关系的影响。研究结果显示:(1)物种多样性与功能多样性正相关,它们与多性状种间差异负相关,而与物种均匀度正相关。物种均匀度是导致功能多样性变化的主要因素,也是导致SD-FD正相关的原因,这是因为随着物种多样性增加,物种均匀度的增加程度大于多性状种间差异的减少程度,因而功能多样性增加,SD-FD正相关;(2)功能多样性指数(FD_(Rao)和FDis)随物种多样性指数(H')减速递增,表明群落存在一定的功能冗余,且功能冗余随物种多样性的增大而增大,但尚未达到产生SD-FD无相关性的极限H'值;(3)功能多样性对高寒草甸生态系统地上净初级生产力(ANPP)的影响大于物种多样性的影响,二元线性回归显示在同时考虑二者对ANPP的影响时,可排除物种多样性的作用。但由于物种多样性下降或物种丧失引起的物种功能性状丢失或性状空间维度减小将导致功能多样性降低,表明它们之间存在一定互补性,在研究生物多样性与生态系统功能关系时,同时考虑物种多样性和功能多样性的影响仍十分必要。     

Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment

Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions. The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients. GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations. The approach can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment.     

Genotypic richness and dissimilarity opposingly affect ecosystem functioning

Biodiversity is an essential determinant of ecosystem functioning. Numerous studies described positive effects of diversity on the functioning of communities arising from complementary resource use and facilitation. However, high biodiversity may also increase competitive interactions, fostering antagonism and negatively affecting community performance. Using experimental bacterial communities we differentiated diversity effects based on genotypic richness and dissimilarity. We show that these diversity characteristics have opposite effects on ecosystem functioning. Genotypic dissimilarity governed complementary resource use, improving ecosystem functioning in complex resource environments. Contrastingly, genotypic richness drove allelopathic interactions, mostly reducing ecosystem functioning. The net biodiversity effect on community performance resulted from the interplay between the genetic structure of the community and resource complexity. These results demonstrate that increasing richness, without concomitantly increasing dissimilarity, can decrease ecosystem functioning in simple environments due to antagonistic interactions, an effect insufficiently considered so far in mechanistic models of the biodiversity-ecosystem functioning relationship.     

Estimating and conserving patterns of invertebrate diversity: a test case of New Zealand land snails

Aim Using New Zealand land snails as a case study, we evaluated recent spatial modelling approaches for the analysis of diversity in species‐rich invertebrate groups. Applications and prospects for improved conservation assessment were investigated. Location New Zealand. Methods The study used a spatially extensive and taxonomically comprehensive, plot‐based dataset on community structure in New Zealand land snails. Generalized regression analysis and spatial prediction (GRASP) was used to model and predict species richness as a function of environmental variables (including aspects of climate, soils and vegetation). Generalized dissimilarity modelling (GDM) was used to model turnover in species composition in relation to environmental and geographical distances, and to assess community similarity and the representativeness of the reserve network. Results Observed land snail richness in 20 × 20 m plots ranged from 1 to 74 (mean 17.5). The GRASP model explained a modest 27% of the variation in richness. The GDM model explained 57% of the variation in species turnover and indicated approximately equal amounts related to environmental (Cody’s beta diversity) and geographical distance (Cody’s gamma diversity). Temperature and moisture were the most important environmental variables. Results indicate that snail distributions are not only sorted by environment but are also strongly influenced by historical effects consistent with those expected of poorly dispersing taxa that have persisted in refugia during past climatic change. The GDM model enabled spatial classifications of snail communities, highlighting diverse communities in heterogeneous regions, such as the South Island mountains, and also enabled continuous depictions of community similarity and adequacy of New Zealand’s protected natural areas network. Main conclusions The GRASP and GDM analyses allowed us to model and depict spatial patterns of diversity in land snail communities involving 845 species, and produce community classifications and estimates of community similarity. These tools advance conservation assessment in species‐rich groups, but require further conceptual and methodological development.     

海口和三亚两城市破碎化林地中鸟类群落多样性与嵌套分布格局

城市化是生物多样性快速丧失的主要原因之一。鸟类作为城市生态系统的重要组成部分, 其生物多样性格局和物种保护已成为城市生态学研究的热点。为揭示城市化过程中城区和郊区破碎化林地中鸟类群落的多样性差异和嵌套格局, 本研究于2021年春、夏季鸟类繁殖期采用样线法对海口和三亚市的城区、郊区共13个林地斑块中的鸟类群落进行调查。使用NODF (nestedness metric based on overlap and decreasing fill)和WNODF (weighted nestedness metric based on overlap and decreasing fill)方法进行嵌套格局分析。研究发现: (1)共记录到林鸟100种, 隶属于11目39科, 其中三亚郊区的鸟类丰富度最高, 共8目29科68种。记录到国家重点保护鸟类共18种, 其中两城市郊区的国家重点保护鸟类物种数均多于城区, 海口郊区还记录到国家I级重点保护鸟类黄胸鹀(Emberiza aureola)。(2)鸟类群落多度、物种丰富度、Pielou均匀度指数和Shannon-Wiener多样性指数在不同区域中均存在差异。海口城区的鸟类群落多度显著高于海口郊区(P < 0.05), 三亚郊区的鸟类群落物种丰富度、Pielou均匀度指数和Shannon-Wiener多样性指数均显著高于三亚城区和海口郊区(P < 0.05)。(3)嵌套分析结果表明, 海口和三亚市的城区、郊区林地鸟类群落均呈现反嵌套分布格局。线性回归分析显示, 三亚市城区和郊区的斑块面积与鸟类物种丰富度呈显著正相关, 而物种丰富度与斑块距最近大面积林地的距离之间无显著相关性。研究表明, 两城市鸟类群落多样性都表现出郊区高于城区的特点, 少数优势种(如白头鹎 Pycnonotus sinensis)占据了城市中的主要生态位。受城市化的影响, 海口郊区与城区鸟类群落有同质化的趋势。鸟类在城区和郊区斑块间的高流动性、种间竞争和斑块中资源的可利用性等因素可能导致斑块间鸟类群落的反嵌套分布格局。我们建议应加强城区和郊区鸟类的保护, 减少对林地的破坏, 提高城市鸟类多样性。     

Environmental drivers of species composition and functional diversity of dung beetles along the Atlantic Forest–Pampa transition zone

Human activities are causing a rapid loss of biodiversity, which impairs ecosystem functions and services. Therefore, understanding which processes shape how biodiversity is distributed along spatial and environmental gradients is a first step to guide conservation and management efforts. We aimed to determine the relative explanatory importance of biogeographic, environmental, landscape and spatial variables on assemblage dissimilarities and functional diversity of dung beetles along the Atlantic Forest–Pampa (i.e. forest–grassland) transition zone located in Southeast South America. We described each site according to their biogeographic position, environmental conditions, landscape features and spatial patterns. The compositional dissimilarity was partitioned into turnover and nestedness components of β‐diversity. Mantel tests and generalised dissimilarity models were used to relate β‐diversity and its components to biogeographic, environmental, landscape and spatial variables. Variation partitioning analysis was used to estimate the pure and shared variation in species composition and functional diversity explained by the four categories of predictors. Biome domain was the main factor causing dung beetle compositional dissimilarity, with a high species replacement between Atlantic Forest and Pampa. Biogeographic, environmental, landscape and spatial distances also affected the patterns of dung beetle dissimilarity and β‐diversity components. The shared effects of the four sets of predictors explained most of the variation in dung beetle composition. A similar response pattern was found for dung beetle functional diversity, which excluded biogeographic effects. Only the pure effects of environmental and spatial predictors were significant for species composition and functional diversity. Our results indicate that dung beetle species composition and functional diversity are jointly driven by environmental, landscape and spatial predictors with higher pure environmental and spatial effects. The forest–grassland transition zone promotes a strong species and trait replacement highly influenced both by environmental filtering and dispersal limitation.     

Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here, we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize vs. potato), soil type (sand vs. clay-textured soils) and habitat (plant root vs. bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species-poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive 'loss' from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass-cropping history together explained 32% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a 'bottleneck effect' on AMF communities through increased stochastic effects under environmental stress.