On the methods to assess significance in nestedness analyses

Use of Z values to evaluate nestedness significance is a common procedure. An appealing alternative to the use of Z values is that of using a value of relative nestedness (RN). However, there is no agreement on the preferable procedures to generate the null matrices needed to compute both Z and RN. In general, it is recommended to use restrictive null models that take into account row and column totals. The two most widely used null models of this kind, namely, FF and CE [that generate matrices with row and column sums equal (FF) or proportional (CE) to the row and column totals of the original matrix, respectively], are very different in terms of restrictiveness. We performed a set of comparative analyses on both theoretical and real matrices to investigate the differences between the use of Z and RN values, and between the use of FF and CE null models, when NODF (Nestedness metric based on overlap and decreasing fill) or ρ(A) (i.e., the largest eigenvalue of the adjacency matrix) are used to measure nestedness. We found no difference in the use of Z or RN values. On the other hand, we found that different combinations of nestedness measures and null models may lead to inconsistent outcomes. Our results offer some clarity on a few issues that, despite playing a central role in the practical application of nestedness analysis, have been little explored, and highlight the need for the definition of some commonly accepted standards.     

Nestedness in insular floras: spatiotemporal variation and underlying mechanisms

Aims Nestedness is a characteristic of insular metacommunity structure. Relatively few studies, however, have attempted to evaluate temporal changes in nestedness, or elucidate the mechanisms underlying nestedness. I evaluated both spatial and temporal patterns of nestedness in the insular floras of four archipelagoes of small islands in the Bahamas and the potential underlying environmental gradients.Methods The NODF (a nestedness metric based on overlap and decreasing fill) and the matrix temperature measure, T, were used to quantify nestedness in insular floras on small islands near Abaco, Andros, Great Exuma and the Exuma Cays, Bahamas. Two different null models were employed for each nestedness measure. Six environmental variables were evaluated in relation to nestedness by ordering islands according to gradients and recalculating NODF scores.Important findings All archipelagoes were significantly nested. Nestedness among sites contributed more to overall nestedness than did nestedness among species. NODF scores varied among archipelagoes, but were surprisingly constant over time. Ordering islands by vegetated area yielded the highest nestedness scores for three archipelagoes; ordering islands by protection from exposure yielded the highest nestedness score for one archipelago. Nestedness scores varied little over time even though species compositions changed, indicating that extinctions occurred in a deterministic manner. The relative importance of area suggests extinction is an important mechanism in producing nestedness. Attempting to determine the relative importance of immigrations or extinctions requires some assumptions, however, and both processes are likely cumulative in most cases.     

Disentangling community patterns of nestedness and species co-occurrence

Two opposing patterns of meta‐community organization are nestedness and negative species co‐occurrence. Both patterns can be quantified with metrics that are applied to presence‐absence matrices and tested with null model analysis. Previous meta‐analyses have given conflicting results, with the same set of matrices apparently showing high nestedness (Wright et al. 1998) and negative species co‐occurrence (Gotelli and McCabe 2002). We clarified the relationship between nestedness and co‐occurrence by creating random matrices, altering them systematically to increase or decrease the degree of nestedness or co‐occurrence, and then testing the resulting patterns with null models. Species co‐occurrence is related to the degree of nestedness, but the sign of the relationship depends on how the test matrices were created. Low‐fill matrices created by simple, uniform sampling generate negative correlations between nestedness and co‐occurrence: negative species co‐occurrence is associated with disordered matrices. However, high‐fill matrices created by passive sampling generate the opposite pattern: negative species co‐occurrence is associated with highly nested matrices. The patterns depend on which index of species co‐occurrence is used, and they are not symmetric: systematic changes in the co‐occurrence structure of a matrix are only weakly associated with changes in the pattern of nestedness. In all analyses, the fixed‐fixed null model that preserves matrix row and column totals has lower type I and type II error probabilities than an equiprobable null model that relaxes row and column totals. The latter model is part of the popular nestedness temperature calculator, which detects nestedness too frequently in random matrices (type I statistical error). When compared to a valid null model, a matrix with negative species co‐occurrence may be either highly nested or disordered, depending on the biological processes that determine row totals (number of species occurrences) and column totals (number of species per site).     

An evaluation of randomization models for nested species subsets analysis

Randomization models, often termed “null” models, have been widely used since the 1970s in studies of species community and biogeographic patterns. More recently they have been used to test for nested species subset patterns (or nestedness) among assemblages of species occupying spatially subdivided habitats, such as island archipelagoes and terrestrial habitat patches. Nestedness occurs when the species occupying small or species-poor sites have a strong tendency to form proper subsets of richer species assemblages. In this paper, we examine the ability of several published simulation models to detect, in an unbiased way, nested subset patterns from a simple matrix of site-by-species presence-absence data. Each approach attempts to build in biological realism by following the assumption that the ecological processes that generated the patterns observed in nature would, if they could be repeated many times over using the same species and landscape configuration, produce islands with the same number of species and species present on the same number of islands as observed. In mathematical terms, the mean marginal totals (column and row sums) of many simulated matrices would match those of the observed matrix. Results of model simulations suggest that the true probability of a species occupying any given site cannot be estimated unambiguously. Nearly all of the models tested were shown to bias simulation matrices toward low levels of nestedness, increasing the probability of a Type I statistical error. Further, desired marginal totals could be obtained only through ad-hoc manipulation of the calculated probabilities. Paradoxically, when such results are achieved, the model is shown to have little statistical power to detect nestedness. This is because nestedness is determined largely by the marginal totals of the matrix themselves, as suggested earlier by Wright and Reeves. We conclude that at the present time, the best null model for nested subset patterns may be one based on equal probabilities of occurrence for all species. Examples of such models are readily available in the literature. Received: 3 February 1997 / Accepted: 21 September 1997     

The relationship between species replacement,dissimilarity derived from nestedness,and nestedness

Aim Beta diversity can be partitioned into two components: dissimilarity due to species replacement and dissimilarity due to nestedness ( Baselga, 2010 , Global Ecology and Biogeography, 19 , 134–143). Several contributions have challenged this approach or proposed alternative frameworks. Here, I review the concepts and methods used in these recent contributions, with the aim of clarifying: (1) the rationale behind the partitioning of beta diversity into species replacement and nestedness‐resultant dissimilarity, (2) how, based on this rationale, numerators and denominators of indices have to match, and (3) how nestedness and nestedness‐resultant dissimilarity are related but different concepts. Innovation The rationale behind measures of species replacement (turnover) dictates that the number of species that are replaced between sites (numerator of the index) has to be relativized with respect to the total number of species that could potentially be replaced (denominator). However, a recently proposed partition of Jaccard dissimilarity fails to do this. In consequence, this partition underestimates the contribution of species replacement and overestimates the contribution of richness differences to total dissimilarity. I show how Jaccard dissimilarity can be partitioned into meaningful turnover and nestedness components, and extend these new indices to multiple‐site situations. Finally the concepts of nestedness and nestedness‐resultant dissimilarity are discussed. Main conclusions Nestedness should be assessed using consistent measures that depend both on paired overlap and matrix filling, e.g. NODF, whereas beta‐diversity patterns should be examined using measures that allow the total dissimilarity to be separated into the components of dissimilarity due to species replacement and dissimilarity due to nestedness. In the case of multiple‐site dissimilarity patterns, averaged pairwise indices should never be used because the mean of the pairwise values is unable to accurately reflect the multiple‐site attributes of dissimilarity.     

Temporal variability of nestedness and idiosyncratic species in stream insect assemblages

Aims The nested subset pattern has been widely studied in the last 20 years, and recent syntheses have challenged the prevalence of this pattern in nature. We examined the degree of nestedness, its temporal variability and its environmental correlates in stream insects of a boreal drainage system. We also examined differences between nested and idiosyncratic species in site occupancy, niche position and niche breadth. Location Koutajoki drainage basin in northern Finland. Methods We used (i) nestedness analyses with three null models for testing the significance of nestedness; (ii) Spearman rank correlation to examine the correlates of nestedness; (iii) outlying mean index analysis to analyse the niche characteristics of species; (iv) and t‐test to examine differences in niche breadth, niche position and site occupancy of idiosyncratic and other nested species. Results Stream insect assemblages were significantly nested in each of the three study years. The maximally packed matrices were significantly nested according to the nestedness calculator based on null models I (species frequencies and site richness equiprobable) and II (species frequencies fixed and site richness equiprobable), but non‐significant based on a conservative null model III (species frequencies and site richness fixed to those of the observed matrix). The most important correlate of nestedness was stream size, whereas isolation, productivity (total phosphorus) and habitat heterogeneity exhibited non‐significant relationship with nestedness. Idiosyncratic species occurred, on average, at more sites than nested species, mirroring the restricted distributions of several nested species that were inclined towards species‐rich sites. Idiosyncratic and nested species also differed in niche position and niche breadth, with idiosyncratic species having, on average, less marginal niche positions and wider niches than nested species. Main conclusions Stream size correlated with nestedness, possibly because small streams were inhabited only by species able to persist under, or colonize shortly after, disturbances, while most species could occur at larger sites where disturbances are less severe. From the conservation perspective, our findings suggest that stream size really matters, given that sites with high species richness and many rare species are more likely to occur in larger streams. However, also the requirements of idiosyncratic species should be accommodated in conservation planning.     

The abundance effect on network nestedness is stronger for parasitic than herbivory interactions

多度对寄生型网络嵌套结构的影响大于食草型网络 因为物种多度显著影响种间互作频率,分析食物网结构对物种多样性和稳定性影响时,应基于能够反映物种真实偏好的网络(即偏好网),而不是直接观察得到的网络(即观察网)。食草网络中(植物为低营养级)的植物资源多度大于寄生网络中(动物为低营养级)寄主资源多度,因此我们假设：寄生网络的结构比食草网络的结构更易受到多度效应的影响。为验证这一假设,我们从已发表的文献中收集了80 个定量观察网络(包括34个植物-食草昆虫网络和46个寄生网络),应用有效多度模型去除物种多度对观察网络的影响,从而得出偏好网络。然后,我们应用weighted NODF和spectral radius两个嵌套系数表征网络嵌套性,分析了观察网和偏好网的物种链接数分布、相互作用均匀度、加权连通度和稳健性的差异。结果表明,在偏好网中,寄生网络的嵌套程度要低于食草网络,这可能是因为去除多度影响增加了种间作用频率的均匀度。偏好网的加权连通度和稳健性显著高于相应的观察网,表明偏好网比观察网具有更高的网络稳定性。未来的食物网研究不仅应关注互惠和拮抗网络的结构差异,还应该关注食草和寄生等不同类型拮抗食物网的结构差异。     

A waterfowl seed-dispersal network from the Neotropical region is nested and modular

Seed dispersal by vertebrates is fundamental for the persistence of plant species, forming networks of interactions that are often nested and modular. Networks involving angiosperms and frugivorous birds are relatively well-studied in the Neotropical region, but there are no previous studies of networks involving waterbirds. Here, we describe the structure of a Neotropical waterfowl seed-dispersal network and identify the species that have an important role for the network structure. We used information on 40 plant taxa found in fecal samples of five common waterfowl species to calculate the nestedness (NODF), weighted nestedness (WNODF), modularity, and weighted modularity of the network. We found that the network was nested, with yellow-billed teal showing the highest contribution both to nestedness and weighted nestedness. Twenty-four plant species contributed positively to weighted nestedness, with Salzmann's mille graines presenting the highest influence both to nestedness and weighted nestedness. The network was modular, but the weighted modularity was not significant. These results need to be considered with caution due to incomplete interaction sampling for two species. Ringed teal, Brazilian teal, and yellow-billed teal were considered hub modular species. Among plants, beak sedges and water snowflake were considered modular hub species, while Salzmann's mille graines and spikerush were network connectors. The structure of this Neotropical waterbird seed-dispersal network differed from the only previous waterfowl network study, from Europe, which found similar level of nestedness but no significant modularity. We include several possible explanations for this discrepancy and identified priorities for future research into waterbird–plant interaction networks. Abstract in Portuguese is available with online material.     

Influence of taxonomic resolution on mutualistic network properties

1. Ecologists are increasingly interested in plant–pollinator networks that synthesize in a single object the species and the interactions linking them within their ecological context. Numerous indices have been developed to describe the structural properties and resilience of these networks, but currently, these indices are calculated for a network resolved to the species level, thus preventing the full exploitation of numerous datasets with a lower taxonomic resolution. Here, we used datasets from the literature to study whether taxonomic resolution has an impact on the properties of plant–pollinator networks.
2. For a set of 41 plant–pollinator networks from the literature, we calculated nine network index values at three different taxonomic resolutions: species, genus, and family. We used nine common indices assessing the structural properties or resilience of networks: nestedness (estimated using the nestedness index based on overlap and decreasing fill [NODF], weighted NODF, discrepancy [BR], and spectral radius [SR]), connectance, modularity, robustness to species loss, motifs frequencies, and normalized degree.
3. We observed that modifying the taxonomic resolution of these networks significantly changes the absolute values of the indices that describe their properties, except for the spectral radius and robustness. After the standardization of indices measuring nestedness with the Z‐score, three indices—NODF, BR, and SR for binary matrices—are not significantly different at different taxonomic resolutions. Finally, the relative values of all indices are strongly conserved at different taxonomic resolutions.
4. We conclude that it is possible to meaningfully estimate the properties of plant–pollinator interaction networks with a taxonomic resolution lower than the species level. We would advise using either the SR or robustness on untransformed data, or the NODF, discrepancy, or SR (for weighted networks only) on Z‐scores. Additionally, connectance and modularity can be compared between low taxonomic resolution networks using the rank instead of the absolute values.

     

Nestedness and τ-temperature in ecological networks

The τ-temperature is a measure of disorder of bipartite networks that is based on the total Manhattan distance of the adjacency matrix. Two properties of this measure are that it does not depend on permutations of lines or columns that have the same connectivity and it is completely determined by connectivities of lines and columns. The normalisation of τ is done by an uniform random matrix whose elements were previously sorted. τ shows no bias against uniform random matrices of several occupations, ρ, sizes, L, and shapes. The scaling of the total Manhattan distance of a random matrix is D_rand ∝ L³ρ while the same scaling for a full nested matrix is D_nest ∝ L³ρ^3/2. We test τ for a large set of empirical matrices to verify these scalings. The index τ correlates better with the temperature of Atmar than with the NODF index of nestedness. We conclude this work by discussing differences between nestedness indices and order/disorder indices.     

A comparative analysis of nested subset patterns of species composition

We present a broad comparative assessment of nested subsets in species composition among ecological communities. We assembled presence-absence data from a broad range of taxa, geographic regions, and spatial scales; and subjected this collection of datasets to common analyses, including a variety of metrics for measuring nestedness and null hypotheses against which to evaluate them. Here we identify ecological patterns in the prevalence and strength of nested subset structure, and assess differences and biases among the available methodologies. In all, we compiled 279 presence-absence matrices, of which 163 do not overlap in their coverage of species and sites. The survey includes studies on vertebrates, arthropods, mollusks, plants, and other taxa; from north temperate, tropical, and south temperate latitudes. Our results were as follows. Statistically significant nestedness was common. Assemblages from landbridge archipelagos were strongly nested, and immigration experiments were least nested. This adds further empirical support to the hypothesis that extinction plays a major role in producing nested structure. Nestedness was positively correlated with the ratio of the areas of the largest and smallest sites, suggesting that the range in area of sites affects nestedness. Taxonomic differences in nestedness were weak. Higher taxonomic levels showed stronger nesting than their constituent lower taxa. We observed no effect of distance of isolation on nestedness; nor any effects of latitude. With regard to methodology, the metrics Nc and Ut yielded similar results, although Nc proved slightly more flexible in use, and deals differently with tied sites. Similarities also exist in the behavior of N0 (“N”) and Up, and between N1 and Ua. Standardized nestedness metrics were mostly insensitive to matrix size, and were useful in comparative analyses among presence-absence matrices. Most metrics were affected by the proportion of presences in the matrix. All analyses of nestedness, therefore, should test for bias due to matrix fill. We suggest that the factors controlling nested subset structure can be thought of as four filters that species pass to occur at a site: a sampling filter, a distance filter, a habitat filter, and an area filter – and three constraints on community homogeneity: evolutionary history, recent history, and spatial variation in the environment. The scale of examination can also have important effects on the degree of nestedness observed. Received: 13 September 1996 / Accepted: 16 September 1997     

Nestedness and niche‐based species loss in moorland plant communities

Communities in isolated habitat patches surrounded by inhospitable matrices often form a nested subset pattern. However, the underlying causal mechanisms and conservation implications of nestedness in regional communities remain controversial. The nested ranks of species in a nested species‐by‐site matrix may reflect a gradient of species vulnerability to extinction or of colonization ability. However, nestedness analysis has rarely been used to explore determinants of species rank; consequently, little is known of underpinning mechanisms. In this study, we examined nestedness in moorland plant communities widely interspersed within the subalpine zone of northern Japan. Moorland sites differed in area (1000–160 000 m²) and were naturally isolated from one another to various extents within an inhospitable forest matrix. We also determined whether site characteristics (physical and morphometric measures) and species characteristics (niche position and breadth, based on species’ traits) are related to nestedness. Moorland plant communities in the study area were significantly nested. The pH and moorland kernel density (proxy for spatial clustering of moorlands around the focal site) were the most important predictors of moorland site nested rank in a nestedness matrix. Niche breadths of species (measured as variation in leaf mass area and height) predicted species’ nested ranks. Selective environmental tolerances imposed by environmental harshness and selective extinction caused by declines in site carrying capacities probably account for the nested subset pattern in moorland plant communities. The nested rank of species in the nestedness matrix can therefore be translated into the potential order of species loss explainable by species niche breadths (based on variation in functional traits). Complementary understanding of the determinants of site ranking and species ranking in the nestedness matrix provides powerful insight into ecological processes underlying nestedness and into the ways by which communities are assembled or disassembled by such processes.     

Ecological traits reveal functional nestedness of bird communities in habitat islands: a global survey

The widespread destruction and fragmentation of natural habitats around the world creates a strong incentive to understand how species and communities respond to such pressures. The vast majority of research into habitat fragmentation has focused solely on species presence or absence. However, analyses using innovative functional methodologies offer the prospect of providing new insights into the key questions surrounding community structure in fragmented systems. A key topic in fragmentation research is nestedness (i.e. the ordered composition of species assemblages involving a significant tendency for packing of the presence–absence matrix into a series of proper subsets). To date, nestedness analyses have been concerned solely with nestedness of species membership. Here, we capitalize on the publication of a recent nestedness index (traitNODF) in which the branch lengths of functional dendrograms are incorporated into the standard NODF nestedness index. Using bird community data from 18 forest‐habitat‐island studies, and measurements of eight continuous functional traits from over 1000 bird species, we conduct the first synthetic analysis of nestedness from a functional perspective (i.e. a nestedness analysis which incorporates how similar species are in terms of their ecological traits). We use two null models to test the significance of any observed functional nestedness, and investigate the role of habitat island area in driving functional nestedness. We also determine whether functional nestedness is driven primarily by species composition or by differences in species’ traits. We found that the majority (94%) of datasets were functionally nested by island area when a permutation null model was used, although only 11–22% of datasets were significantly functionally nested when a more conservative fixed‐fixed null model was used. Species composition was always the most important driver of functional nestedness, but the effect of differences in species traits was occasionally quite large. Our results isolate the importance of island area in driving functional nestedness where it does occur and show that habitat loss results in the ordered loss of functional traits. This analysis demonstrates the potential insights that may derive from testing for ordered patterns of functional diversity. Synthesis The widespread fragmentation of natural habitats around the world creates a strong incentive to understand how ecological communities respond to such pressures. A key topic in this research agenda is nestedness; however, to date, nestedness analyses have been concerned solely with species presence or absence. Using data from 18 bird‐habitat‐island studies we conduct the first synthetic analysis of nestedness from a functional perspective (i.e. a nestedness analysis which incorporates how similar species are in terms of their ecological traits). Our findings suggest that many bird‐habitat island communities are significantly functionally nested, although our results were sensitive to the null model used. Our study demonstrates the benefits of testing for ordered patterns of functional diversity.     

Trapped in the web of water: Groundwater‐fed springs are island‐like ecosystems for the meiofauna

We investigated whether the equilibrium theory of island biogeography (ETIB) can be applied to the meiofauna of groundwater‐fed springs. We tested whether copepod species richness was related with spring area, discharge, and elevation. Additionally, five hypotheses are tested based on species distribution patterns, dispersal ability, and life‐history characteristics of several guilds (stygobiotic, nonstygobiotic, cold stenotherm, and noncold stenotherm species). Thirty springs in the central Apennines (Italy) were considered. A multimodel selection procedure was applied to select best‐fit models using both ordinary least‐squares regressions and autoregressive models. Mantel tests were used to investigate the impact of spatial autocorrelation in determining interspring similarity (ßsor), pure turnover (ßsim), intersite nestedness (ßnest = ßsor ? ßsim), and matrix nestedness (measured using NODF and other metrics). Explicit consideration of spatial correlations reduced the importance of predictors of overall species richness, noncold stenotherm species (both negatively affected by elevation), cold stenotherm species, and nonstygobiotic species, but increased the importance of area for the stygobiotic species. We detected nested patterns in all cases, except for the stygobites. Interspring distances were positively correlated with ßsor and ßnest (but not with ßsim) for the entire data set and for nonstygobiotic, cold stenotherm, and noncold stenotherm species. In the case of stygobites, interspring geographical distances were marginally correlated with ßsor and no correlation was found for ßsim and ßnest. We found support for ETIB predictions about species richness, which was positively influenced by area and negatively by elevation (which expresses the size of source of immigrants). Low turnover and high nestedness are consistent with an equilibrium scenario mainly regulated by immigration and extinction. Stygobites, which include many distributional and evolutionary relicts, have a low capability to disperse through the aquifers and tend to be mainly confined to the springs where they drifted out and were trapped by springbed sediments.     

A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement

Nestedness has been widely reported for both metacommunities and networks of interacting species. Even though the concept of this ecological pattern has been well-defined, there are several metrics by which it can be quantified. We noted that current metrics do not correctly quantify two major properties of nestedness: (1) whether marginal totals (i.e. fills) differ among columns and/or among rows, and (2) whether the presences (1's) in less-filled columns and rows coincide, respectively, with those found in the more-filled columns and rows. We propose a new metric directly based on these properties and compare its behavior with that of the most used metrics, using a set of model matrices ranging from highly-nested to alternative structures in which no nestedness should be detected. We also used an empirical dataset to explore possible biases generated by the metrics as well as to evaluate correlations between metrics. We found that nestedness has been quantified by metrics that inappropriately detect this pattern, even for matrices in which there is no nestedness. In addition, the most used metrics are prone to type I statistical errors while our new metric has better statistical properties and consistently rejects a nested pattern for different types of random matrices. The analysis of the empirical data showed that two nestedness metrics, matrix temperature and the discrepancy measure, tend to overestimate the degrees of nestedness in metacommunities. We emphasize and discuss some implications of these biases for the theoretical understanding of the processes shaping species interaction networks and metacommunity structure.     

A protocol to compare nestedness among submatrices

Searching for nestedness has become a popular exercise in community ecology. Significance of a nestedness index is usually evaluated using z values, and finding that a matrix is nested is typically a common result. However, nestedness is not likely to be spread uniformly within a matrix of species presence/absence per site. Selected parts of the matrix may show a degree of nestedness significantly higher (or lower) than expected from the overall pattern. Here we describe a procedure to assess if a particular submatrix (i.e., a peculiar combination of rows and columns extracted from the complete matrix) is more or less nested than expected for an assortment of sites and species taken at random from the same overall matrix. The idea is to obtain several submatrices of different sizes from the same overall matrix and to calculate their z values. A regression is then performed between z values of submatrices and their sizes. A nestedness index independent of matrix size is suggested as the deviation of the z value of a particular submatrix from that expected according to the regression line. We applied our protocol to 55 matrices with different nestedness indices under various null-models and, for purpose of demonstration, we discussed in detail a single case study regarding various animal groups of the Aegean Islands (Greece). The obtained results strongly encourage further research to focus not only on the question whether a matrix is nested or not, but also on where and why nestedness is confined.     

The Rapoport effect is detected in a river system and is based on nested organization

Aim To test two hypotheses: (i) the Rapoport effect is valid for a river continuum, particularly regarding the altitudinal distribution of mayflies over the large‐scale continuum from alpine stream to medium‐sized lowland river, and (ii) the observed Rapoport effect is based on high nestedness of the meta‐assemblage, implying the presence of a common species pool and species‐thinned nested subsets. Location Geometric centre of Eurasia, south‐western Siberia, Russia. Methods Regression analysis of breadth and midpoints of species altitudinal ranges, species richness and altitude. Comparison of the observed patterns with the null model predicted by the mid‐domain effect and conventional null hypothesis. Nestedness analysis. Results The Rapoport effect was explicitly demonstrated: species altitudinal ranges expanded with increase in the ranges’ midpoints and average per‐altitude ranges increased with increase in altitude and concurrent decrease in species richness. The significance of each trend was confirmed with respect to both the null models applied. Nestedness analysis has revealed that the observed Rapoport effect is based on nested organization of the meta‐assemblage over the river altitudinal/longitudinal gradient: a common species pool at low (but not the lowest) altitudes and nested subsets of this pool at higher altitudes. Main conclusions This study for the first time credibly shows the altitudinal Rapoport effect in freshwaters. This finding demonstrates cross‐habitat‐type consistency of the Rapoport effect, but does not suggest that the Rapoport effect is an obligatory attribute of river systems or lotic organisms. High nestedness underlying the observed Rapoport effect together with some previous studies indicate that the Rapoport effect in altitudinal and bathymetric gradients in general may be based on nested organization. The study highlights a deficiency of cross‐habitat‐type analyses of macroecological patterns (i.e. over terrestrial, freshwater and marine habitats).     

Rethinking the relationship between nestedness and beta diversity: a comment on Baselga (2010)

Baselga [Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19 , 134–143, 2010] proposed pairwise (β_nes) and multiple‐site (β_NES) beta‐diversity measures to account for the nestedness component of beta diversity. We used empirical, randomly created and idealized matrices to show that both measures are only partially related to nestedness and do not fit certain fundamental requirements for consideration as true nestedness‐resultant dissimilarity measures. Both β_nes and β_NES are influenced by matrix size and fill, and increase or decrease even when nestedness remains constant. Additionally, we demonstrate that β_NES can yield high values even for matrices with no nestedness. We conclude that β_nes and β_NES are not true measures of the nestedness‐resultant dissimilarity between sites. Actually, they quantify how differences in species richness that are not due to species replacement contribute to patterns of beta diversity. Finally, because nestedness is a special case of dissimilarity in species composition due to ordered species loss (or gain), the extent to which differences in species composition is due to nestedness can be measured through an index of nestedness.     

Nestedness of north-west European land snail ranges as a consequence of differential immigration from Pleistocene glacial refuges

We investigated whether ranges in continental biota are nested. We propose a test for nested subset structure which can detect nestedness even if there are several sets of nested subsets as expected on a larger geographical scale. The test is based on a Monte Carlo simulation with a null model that considers spatial autocorrelation of the occurrences of a taxon. The number of cases in which the occurrences of a species form a subset of the occurrences of another species is used as test statistic. In a case study we show that the ranges of north-west European land snail species are significantly nested. The geographic centres of the sets of nested subsets correlate with glacial refuges. The differential immigration of taxa restricted to southern refuges during the glacials was probably an important mechanism resulting in the observed nestedness of the ranges of the north-west European land snail species. Some species which were more widespread during Pleistocene glacials contribute little to the nested subset pattern and are not nested among themselves. A comparison between groups of species differing in their dispersal abilities indicates that differences in the degree of nestedness are primarily due to differences in the variance of range sizes and not in dispersal abilities. We found a very weak correlation between dispersal ability and the rank of ranges in the sets of nested subsets indicating that nestedness might in part be caused by differential dispersal abilities. We assume that the graded variation of environmental parameters might be more important in generating the nestedness of ranges of north-west European land snail species than their differential dispersal abilities.     

Terrestrial bird community patterns on the coralline islands of the Dahlak Archipelago, Red Sea, Eritrea

Aim This study aims to explain the patterns of species richness and nestedness of a terrestrial bird community in a poorly studied region. Location Twenty‐six islands in the Dahlak Archipelago, Southern Red Sea, Eritrea. Methods The islands and five mainland areas were censused in summer 1999 and winter 2001. To study the importance of island size, isolation from the mainland and inter‐island distance, I used constrained null models for the nestedness temperature calculator and a cluster analysis. Results Species richness depended on island area and isolation from the mainland. Nestedness was detected, even when passive sampling was accounted for. The nested rank of islands was correlated with area and species richness, but not with isolation. Idiosyncrasies appeared among species‐poor and species‐rich islands, and among common and rare species. Cluster analysis showed differences among species‐rich islands, close similarity among species‐poor and idiosyncratic islands, and that the compositional similarity among islands decreased with increasing inter‐island distance. Thus, faunas of species‐poor, smaller islands were more likely to be subsets of faunas of species‐rich, larger islands if the distance between the islands was short. Main conclusions Species richness and nestedness were related to island area, and nestedness also to inter‐island distances but not to isolation from the mainland. Thus, nestedness and species richness are not affected in the same way by area and distance. Moreover, idiosyncrasies may have been the outcome of species distributions among islands being influenced also by non‐nested distributions of habitats, inter–specific interactions, and differences in species distributions across the mainland. Idiosyncrasies in nested patterns may be as important as the nested pattern itself for conservation – and conservation strategies based on nestedness and strong area effects (e.g. protection of only larger islands) may fail to preserve idiosyncratic species/habitats.