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.     

Nestedness and migratory status of avian assemblages in North America and Europe

We examine patterns of nestedness and species incidence for the resident and migrant components of avifaunas in North America and Europe. While all assemblages were significantly nested, there were no significant differences between North American and European avifaunas overall in nestedness or incidence. Residents did not differ from migrants in their adherence to a nested distribution, but did exhibit significantly higher incidences when continental affiliation was ignored.¶We develop a new nestedness index that examines each species' relative contribution to an assemblage's overall pattern of nestedness. The relative nestedness index exhibits a quadratic relationship with incidence such that species with low incidences and species with high incidences generally increase the overall level of nestedness, while species with intermediate incidence tend to decrease nestedness.     

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.     

Using intraspecific variation of functional traits and environmental factors to understand the formation of nestedness patterns of a local forest community

从功能性状的种内变异和环境因子的角度理解局域森林群落嵌套格局的成因     

The influence of colonization in nested species subsets

Biotic communities inhabiting collections of insular habitat patches often exhibit compositional patterns described as nested subsets. In nested biotas, the assemblages of species in relatively depauperate sites comprise successive subsets of species in relatively richer sites. In theory, nestedness may result from selective extinction, selective colonization, or other mechanisms, such as nested habitats. Allopatric speciation is expected to reduce nestedness. Previous studies, based largely on comparisons between land-bridge and oceanic archipelagos, have emphasized the role of selective extinction. However, colonization could also be important in generating strong patterns of nestedness. We apply a recently published index of nestedness to more than 50 island biogeographic data sets, and examine the roles of colonization, extinction, endemism, and, to a limited extent, habitat variability on the degree on nestedness. Most data sets exhibit a significant degree of nestedness, although there is no general tendency for land-bridge biotas to appear more nested than oceanic ones. Endemic species are shown to generally reduce nestedness. Comparisons between groups of non-endemic species differing in overwater or inter-patch dispersal ability indicate that superior dispersers generally exhibit a greater degree of nestedness than poorer dispersers, a result opposite that expected if colonization were a less predictable process than extinction. These results suggest that frequent colonization is likely to enhance nestedness, thereby increasing the compositional overlap among insular biotas. The prevalence of selective extinction in natural communities remains in question. The importance of colonization in generating and maintaining nested subsets suggests that (1) minimum critical areas will be difficult to determine from patterns of species distributions on islands; (2) multiple conservation sites are likely to be required to preserve communities in subdivided landscapes; and (3) management of dispersal processes may be as important to preserving species and communities as is minimizing extinctions.     

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     

Differences in habitat quality explain nestedness in a land snail meta-community

We set up two alternative hypotheses on how environmental variables could foster nestedness; one of “nested habitats” and another of “nested habitat quality”. The former hypothesis refers to situations where the nestedness of species depends on a nestedness of discrete habitats. The latter considers situations where all species in an assemblage increase in abundance along the same environmental gradient, but differ in specialisation or tolerance. We tested whether litter‐dwelling land snails (terrestrial gastropods) in boreal riparian forest exhibited a nested community structure, whether such a pattern was related to differences in environmental variables among sites, and which of the two hypotheses that best could account for the found pattern. We sampled litter from 100 m² plots in 29 mature riparian forest sites along small streams in the boreal zone of Sweden. The number of snail species varied between 3 and 14 per site. Ranking the species‐by‐site matrix by PCA scores of the first ordination axis revealed a similarly significant nested pattern as when the matrix was sorted by number of species, showing that the species composition in this meta‐community can be properly described as nested. Several environmental variables, most notably pH index, were correlated with the first PCA axis. All but two species had positive eigenvectors in the PCA ordination and the abundance increased considerably along the gradient for most of the species implying that the hypothesis of “nested habitats” was rejected in favour of the “nested habitat quality” hypothesis. Analyses of nestedness have seldom been performed on equal sized plots, and our study shows the importance of understanding that variation in environmental variables among sites can result in nested communities. The conservation implications are different depending on which of our two hypotheses is supported; a conservation focus on species “hotspots” is more appropriate if the communities are nested because of “nested habitat quality”.     

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.     

Does variation in patch use among butterfly species contribute to nestedness at fine spatial scales?

A nested pattern occurs whenever the species observed in depauperate habitat patches are a subset of those found in more species‐rich patches. Ecologists have documented many instances of nestedness caused by population‐level processes such as colonization and extinction at biogeographic scales. However, few researchers have examined whether nestedness may exist at fine scales due to the ways in which individual organisms discriminate among potential habitat patches. In 1999, we experimentally fragmented an old‐field habitat into patches of varying size to test whether nestedness could exist on a fine spatial scale. Five treatments of differing patch size were replicated five times in a Latin square design by selectively mowing 15×15 m² plots within an old‐field (patch areas: 225, 180, 135, 90, and 45 m²). Specifically, we tested whether butterflies foraging within a network of patches differing in area conformed to a nested subset structure. We also classified species according to (1) their flight height while foraging (high or low), and (2) their adult habitat breadth (ubiquitous, general, or restricted) to determine whether nestedness could be explained by difference in species’ tendency to discriminate among patches differing in area.
We found significant evidence that a community of foraging Lepidoptera conformed to a nested subset structure based on the difference between the observed nestedness within the butterfly community and the nestedness obtained from randomly generated species presence/absence matrices. Poisson regression analyses demonstrated that high‐flying, habitat‐restricted species avoided the smallest patches (90 and 45 m²) in favor of larger remnants, whereas low‐flying, habitat generalists used all patch sizes. Thus, our study is one of the first to demonstrate that nestedness among species subsets can be observed at fine spatial scales (within a single 1.5 hectare field) and may be maintained by species behavioral differences: discriminating species (i.e. high‐flying, habitat restricted) avoided the smallest patches, and less discriminating species (i.e. low‐flying, ubiquitous) were distributed throughout the field without regard to patch size. Our results also suggest that nestedness should be viewed as yet another scalar pattern in ecology, generated by variation in patch use by individuals at fine‐scales as well as the more traditionally invoked processes of extinction and colonization of species at broad‐scales.     

Spatio-temporal nested patterns in macroinvertebrate assemblages across a pond network with a wide hydroperiod range

Nestedness has been widely used to measure the structure of biological communities and occurs when species-poor sites contain subsets of species-rich ones. Here, we examine nested patterns across the macroinvertebrate assemblages of 91 ponds in Doñana National Park, Spain, and explore temporal variation of nestedness and species richness in 19 temporary ponds over 2 years with differing rainfall. Macroinvertebrate assemblages were significantly nested; both pond spatial arrangement and environmental variation being important in driving nested patterns. Despite the nested structure observed, a number of taxa and ponds deviate from this pattern (termed idiosyncratic), by occurring more frequently than expected in species-poor sites, or having assemblages dominated by species largely absent from species-rich sites. Aquatic adults of winged insects, capable of dispersal, were more highly nested than non-dispersing taxa and life-history stages. Idiosyncratic taxa were found in ponds spanning a wide range of hydroperiods, although nestedness was higher in more permanent waterbodies. Monthly sampling demonstrated a gradual increase of species richness and nestedness from pond filling to April–May, when the most temporary ponds started to dry. Although the degree of nestedness of individual pond assemblages varied from month to month, the overall degree of nestedness in the two study years was practically identical despite marked differences in hydroperiod. Our results suggest that differential colonization and environmental variation are key processes driving the nested structure of Doñana ponds, that macroinvertebrate assemblages change in a predictable manner each year in response to cycles of pond wetting and drying, and that connectivity and environmental variability maintain biodiversity in pond networks.     

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.     

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.     

Nested bird and micro-habitat assemblages in a peatland archipelago

Biotic assemblages of insular habitats are nested when poor assemblages are subsets of richer ones. Nestedness of species assemblages is frequent and may result from selective extinction or frequent colonization in insular habitats. It may also be created by a nested distribution of habitats among islands or by sampling bias. We sampled 67 isolated peatlands (7–843 ha) in southern Quebec, Canada, to measure nestedness of bird species assemblages among peatlands and assess the habitat nestedness hypothesis. Species and microhabitat assemblages were both strongly nested among peatlands. Whether sites were ranked by species richness, microhabitat richness or peatland area had no effect on nestedness. However, microhabitat nestedness was significantly reduced when sites were sorted by area rather than by microhabitat richness. As expected, if bird-microhabitat associations are responsible for the nested pattern of distribution, we found a positive correlation between the contributions of bird species and microhabitats to individual site nestedness. Nevertheless, microhabitat assemblages were significantly less nested than bird species assemblages, possibly because of frequent recolonization by birds or uneven sampling among sites. Received: 12 June 1998 / Accepted: 20 September 1998     

Temporal dynamics and nestedness of an oceanic island bird fauna

Aim To examine temporal variation in nestedness and whether nestedness patterns predict colonization, extinction and turnover across islands and species. Location Dahlak Archipelago, Red Sea. Method The distributions of land birds on 17 islands were recorded in two periods 30 years apart. Species and islands were reordered in the Nestedness Temperature Calculator, software for assessing degrees of nestedness in communities. The occupancy probability of each cell, i.e. species–island combinations, was calculated in the nested matrix and an extinction curve (boundary line) was specified. We tested whether historical and current nested ranks of species and islands were correlated, whether there was a relationship between occupancy probability (based on the historical data) and number of extinctions or colonizations (regression analyses) and whether the boundary line could predict extinctions and colonizations (chi‐square analyses). Results Historical and current nested ranks of islands and species were correlated but changes in occupancy patterns were common, particularly among bird species with intermediate incidence. Extinction and turnover of species were higher for small than large islands, and colonization was negatively related to isolation. As expected, colonizations were more frequent above than below the boundary line. Probability of extinction was highest at intermediate occupancy probability, giving a quadratic relationship between extinction and occupancy probability. Species turnover was related to the historical nested ranks of islands. Colonization was related negatively while extinction and occupancy turnover were related quadratically to historical nested ranks of species. Main conclusions Some patterns of the temporal dynamics agreed with expectations from nested patterns. However, the accuracy of the predictions may be confounded by regional dynamics and distributions of idiosyncratic, resource‐limited species. It is therefore necessary to combine nestedness analysis with adequate knowledge of the causal factors and ecology of targeted species to gain insight into the temporal dynamics of assemblages and for nestedness analyses to be helpful in conservation planning.     

The nested structure of marine cleaning symbiosis: is it like flowers and bees?

In a given area, plant-animal mutualistic interactions form complex networks that often display nestedness, a particular type of asymmetry in interactions. Simple ecological and evolutionary factors have been hypothesized to lead to nested networks. Therefore, nestedness is expected to occur in other types of mutualisms as well. We tested the above prediction with the network structure of interactions in cleaning symbiosis at three reef assemblages. In this type of interaction, shrimps and fishes forage on ectoparasites and injured tissues from the body surface of fish species. Cleaning networks show strong patterns of nestedness. In fact, after controlling for species richness, cleaning networks are even more nested than plant-animal mutualisms. Our results support the notion that mutualisms evolve to a predictable community-level structure, be it in terrestrial or marine communities.     

False Correlates of Nested Patterns: A Case Study Using Temporary Pond Microcrustaceans

Nestedness analysis is a popular tool for inferring spatial species distributions, and therefore has management and conservation relevance. Ecologists frequently compute nestedness and subsequently use Spearman rank correlations for inferring relationships between the observed nested ranks of sites with biogeographic and environmental variables. Using temporary pond microcrustaceans hatched from microcosms as a case study, this paper shows that the application of this method can be problematic. While the overall degree and significance of nestedness was robust against a statistical error, the results obtained from randomly generated matrices, in which community structure from the original microcrustacean incidence matrix was maintained (fixed rows –fixed columns constraints), showed that rank correlations of observed nested patterns can be vulnerable to a Type 1 error (detecting an effect when there is none). Using expected nestedness patterns derived from rarefied original matrices to control for sample size effects did not change this result. This problem may have arisen as a result of a quantitative bias related to the disproportionate impact of rank positions of individual ponds in the analysis. Future extensive simulations studies, involving different community structures, should help identify the general reliability of rank correlation results in nestedness analyses. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

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.     

Toward ecologically explicit null models of nestedness

A community is "nested" when species assemblages in less rich sites form nonrandom subsets of those at richer sites. Conventional null models used to test for statistically nonrandom nestedness are under- or over-restrictive because they do not sufficiently isolate ecological processes of interest, which hinders ecological inference. We propose a class of null models that are ecologically explicit and interpretable. Expected values of species richness and incidence, rather than observed values, are used to create random presence-absence matrices for hypothesis testing. In our examples, based on six datasets, expected values were derived either by using an individually based random placement model or by fitting empirical models to richness data as a function of environmental covariates. We describe an algorithm for constructing unbiased null matrices, which permitted valid testing of our null models. Our approach avoids the problem of building too much structure into the null model, and enabled us to explicitly test whether observed communities were more nested than would be expected for a system structured solely by species-abundance and species-area or similar relationships. We argue that this test or similar tests are better determinants of whether a system is truly nested; a nested system should contain unique pattern not already predicted by more fundamental ecological principles such as species-area relationships. Most species assemblages we studied were not nested under these null models. Our results suggest that nestedness, beyond that which is explained by passive sampling processes, may not be as widespread as currently believed. These findings may help to improve the utility of nestedness as an ecological concept and conservation tool.     

Host–parasite nestedness: A result of co-evolving trait-values

Nestedness is an intriguing feature of ecological networks, where those species found in species-depauperate communities are subsets of those found in communities with greater species richness. For bipartite interaction networks, a “community” of species may be thought of as all those pollinating a particular plant, or infecting a particular host, for example. While there is much clear evidence for nestedness in mutualistic webs, host–parasite webs have proven more contentious. There have been a number of suggested causes for nestedness, including an association between the abundance of individuals and the resulting number of species interactions, and the matching of phenotypic traits between species. Questions remain as to the relative importance of these driving factors, especially as host–parasite and mutualistic webs contain completely different interaction types.We propose a model motivated by both of the above factors, considering a trade-off in resources that a species faces in optimizing its transmission or defense. We construct a multi-species model in which both hosts and parasites have limited resources with which to attack or defend themselves from each other. We analyze the evolution of the manner in which they use these resources using adaptive dynamics, to arrive at a final species interaction matrix, which we then test for nestedness. A general model with m hosts and n microparasite species is described here, but results are given for m = n = 5, chosen to be a large enough system for patterns to be identified, but not so large that computational time becomes prohibitive.Our results demonstrate that this co-evolution leads to an unusual amount of nestedness when the trade-offs in transmission for parasites are concave, and an unusual amount of anti-nestedness when they are convex. This enables us to predict the circumstances under which we would expect to observe nestedness in real networks.     

Patterns of Assemblage Structure Indicate a Broader Conservation Potential of Focal Amphibians for Pond Management

Small freshwater ponds host diverse and vulnerable biotic assemblages but relatively few conspicuous, specially protected taxa. In Europe, the amphibians Triturus cristatus and Pelobates fuscus are among a few species whose populations have been successfully restored using pond restoration and management activities at the landscape scale. In this study, we explored whether the ponds constructed for those two target species have wider conservation significance, particularly for other species of conservation concern. We recorded the occurrence of amphibians and selected aquatic macro-invertebrates (dragonflies; damselflies; diving beetles; water scavenger beetles) in 66 ponds specially constructed for amphibians (up to 8 years post construction) and, for comparison, in 100 man-made ponds (created by local people for cattle or garden watering, peat excavation, etc.) and 65 natural ponds in Estonia. We analysed nestedness of the species assemblages and its dependence on the environment, and described the co-occurrence patterns between the target amphibians and other aquatic species. The assemblages in all ponds were significantly nested, but the environmental determinants of nestedness and co-occurrence of particular species differed among pond types. Constructed ponds were most species-rich irrespective of the presence of the target species; however, T. cristatus was frequent in those ponds and rare elsewhere, and it showed nested patterns in every type of pond. We thus conclude that pond construction for the protected amphibians can serve broader habitat conservation aims in the short term. However, the heterogeneity and inconsistent presence of species of conservation concern observed in other types of ponds implies that long-term perspectives on pond management require more explicit consideration of different habitat and biodiversity values. We also highlight nestedness analysis as a tool that can be used for the practical task of selecting focal species for habitat conservation.