Null model tests of clustering of species, negative co-occurrence patterns and nestedness in meta-communities

We propose tests for patterns in meta-community structure. The tests for clustering and nestedness of the occurrences of species and negative co-occurrence patterns provide four important innovations. Firstly, they are not restricted to the analysis of communities along one-dimensional gradients or to the main axis of variation. Secondly, abundance data can also be considered in the null model whereas most previous approaches could consider only presence/absence data. And thirdly, habitat suitability and spatial autocorrelation can be incorporated in the null model so that patterns that might be caused by biotic interactions can be distinguished from patterns which are the result of differences in the suitability or accessibility of sites for the examined organisms. Finally, the test for nestedness is also appropriate if there is more than one set of nested subsets. A re-analysis of 35 data sets with these tests showed the importance of considering the autocorrelation of the occurrences of species in analyses of meta-community structure and demonstrated the advantage of abundance data for tests of clustering of species. With abundance data it could be shown that there is a significant clustering of species, i.e. there are positive associations of species in most meta-communities, even if an environmentally or spatially constrained null model is used for the test. Co-occurrence patterns that might indicate interspecific competition were found in many of the analysed presence/absence data sets. Surprisingly the analysis of abundance data sets provides less evidence for interspecific competition. A hierarchical organization of communities, i.e. nestedness, turned out to be a rare pattern, if the autocorrelation of the occurrences of species is considered.     

Fish larvae-environment networks: co-occurrence patterns,nestedness and robustness of reproductive guilds

Hydrobiologia - We assessed the importance of different types of riverine environments (river channels, tributaries, and floodplain lagoons) for the early development of fish larvae from different...     

Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species

Flowers’ fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success—both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.     

Composition and co-occurrence patterns of Phragmites australis rhizosphere bacterial community

Aquatic Ecology - High oxygen levels and root exudates together provide a resource-enriched habitat for rhizosphere microbes that, in turn, foster plant growth and perform key ecological functions....     

Root-associated community composition and co-occurrence patterns of fungi in wild grapevine

Crops’ wild relatives host a wide range of microorganisms, including some beneficial species that are not found or are under-represented in the domesticated crops. Our goal was to study the underexplored composition of root-associated fungal communities in endangered wild grapevines. We found high taxonomic diversity representing multiple trophic guilds that include beneficial symbiotrophs and endophytes. Soil factors explain a relatively small part of their overall variability. In contrast, the majority of the associated fungal taxa shows a close fit to the neutral model for prediction of their distributions. Only beneficial arbuscular mycorrhizal fungi and the pathogenic Ilyonectria depart from the neutral distribution model and form intimate interactions with the plant host. In addition, pathogenic fungi rarely occurred in samples that included ectomycorrhizal fungi, which suggested potentially applicable inter-microorganism interactions. High abundance and diversity of fungal endophytes on the wild grapevine roots highlight the need for their careful consideration in future studies.     

Habitat complexity drives the turnover and nestedness patterns in a periphytic algae community

Limnology - Habitat complexity drives aquatic community attributes, including the beta diversity components. We tested the hypothesis that community diversity, richness and density are higher on...     

Disentangling composite colour patterns in a poison frog species

A phylogenetic approach was performed to infer whether variation in conspicuous colour-patterns of a poison frog (Dendrobatidae: Dendrobates tinctorius ) has evolved neutrally or under selection. Colour and pattern were split into components that were separately analysed and subsequently re-grouped via principal component analysis. This revealed four different 'displayed' factors on the dorsal and lateral views versus one 'concealed' factor on the ventral view. Based on the assumption that current patterns of trait variation contain information about the evolutionary history of the phenotype, we correlated these trait components to a neutrally evolving gene fragment (cytochrome b ). The concealed factor was significantly correlated with the marker fragment, which identified it as having evolved under genetic drift. Noncorrelation of all displayed factors with the marker may indicate the evolution of colour patterns on dorsum and flanks under selection. In our example, colour pattern should therefore be regarded as a multicomponent signal system.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 433–444.     

Species co-occurrence, nestedness and guild–environment relationships in stream macroinvertebrates

1. Describing species distribution patterns and the underlying mechanisms is at the heart of ecological research. A number of recent studies have used null model approaches to explore mechanisms behind spatial variation in community structure.
2. However, unexplored questions are the degree to which single guilds of potentially competing stream macroinvertebrate species show: (i) interspecific segregation among-stream sites (i.e. occur together less often than expected by chance), suggesting competitive interactions; (ii) interspecific aggregation (i.e. occur together more often than expected by chance), suggesting similar responses to the environment; (iii) comply with nestedness, suggesting the existence of selective extinctions or colonisations and (iv) show similar environmental relationships.
3. The present analyses showed that guilds of stream macroinvertebrates exhibit non-random co-occurrence patterns that were generally contingent on the weighting of sites by stream size. Despite significant segregation of species, each guild also showed significantly nested patterns. Species richness was correlated with different environmental factors between the guilds, although these correlations were relatively low. By contrast, correlations between the major ordination axes and key environmental variables were slightly stronger in canonical correspondence analysis, and generally the same factors were most strongly correlated with variation in the species composition of each guild.
4. The present findings are the first to show that species within each stream macroinvertebrate guild show significant negative co-occurrence at the among-stream riffle scale. These findings present challenges for future studies that aim to disentangle whether these patterns comply with the habitat checkerboard or the competitive checkerboard explanations.     

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.     

Species co-occurrence: the case of congeneric species and a causal approach to patterns of species association

Aim To test whether congeneric species are significantly associated with one another in space, either positively or negatively. Also, to provide a framework for a causal investigation of co‐occurrence patterns by a parallel comparison of interactions in geographical and ecological data matrices. Location For the analysis of congeneric species’ co‐occurrences we used 30 matrices covering a wide range of taxa and geographical areas, while for the causal investigation we used the distribution of 50 terrestrial isopod species on 20 islands and 264 sampling stations in the central Aegean archipelago, as well as a number of ecological variables for each sampling station. Methods We developed a software program (cooc ) that incorporates the species‐by‐species approach to co‐occurrence analysis using EcoSim's output of prior null model analysis of co‐occurrence. We describe this program in detail, and use it to investigate one of the most common assembly rules, namely, the decreased levels of co‐occurrence among congeneric species pairs. For the causal analysis, we proceed likewise, cross‐checking the results from the geographical and the ecological matrices. There is only one possible combination of results that can support claims for direct competition among species. Results We do not get any strong evidence for widespread competition among congeneric species, while most communities investigated do not show significant patterns of species associations. The causal analysis suggests that the principal factors behind terrestrial isopod species associations are of historical nature. Some exceptional cases are also discussed. Main conclusions Presence/absence data for a variety of taxa do not support the assembly rule that congeneric species are under more intense competition compared to less related species. Also, these same data do not suggest strong interactions among species pairs, regardless of taxonomic status. When significant species associations can be seen in such matrices, they mainly reflect the effects of history or of habitat requirements.     

Complex relationships between species niches and environmental heterogeneity affect species co-occurrence patterns in modelled and real communities

Species co-occurrence analysis is commonly used to assess how interspecific interactions dictate community assembly. Non-random co-occurrences, however, may also emerge from niche differences as well as environmental heterogeneity. The relationships between species co-occurrence patterns, environmental heterogeneity and species niches are not fully understood, due to complex interactions among them. To analyse the relationships among these patterns and processes, I developed synthetic community models and analysed a large dataset of tree species across the conterminous United States. Niche overlap and environmental heterogeneity had significant and contrasting effects on species co-occurrence patterns, in both modelled and real communities. Niche breadth, in turn, affected the effect sizes of both variables on species co-occurrence patterns. The effect of niche breadth on the relationship between co-occurrence and niche overlap was markedly consistent between modelled and real communities, while its effect on the relationship between co-occurrence and environmental heterogeneity was mostly consistent between real and modelled data. The results of this analysis highlight the complex and interactive effects of species niche overlap, niche breadth and environmental heterogeneity on species co-occurrence patterns. Therefore, inferring ecological processes from co-occurrence patterns without accounting for these fundamental characteristics of species and environments may lead to biased conclusions.     

Disentangling the effects of plant species invasion and urban development on arthropod community composition

Urban development and species invasion are two major global threats to biodiversity. These threats often co‐occur, as developed areas are more prone to species invasion. However, few empirical studies have tested if both factors affect biodiversity in similar ways. Here we study the individual and combined effects of urban development and plant invasion on the composition of arthropod communities. We assessed 36 paired invaded and non‐invaded sample plots, invaded by the plant Antigonon leptopus, with half of these pairs located in natural and the other half in developed land‐use types on the Caribbean island of St. Eustatius. We used several taxonomic and functional variables to describe community composition and diversity. Our results show that both urban development and A. leptopus invasion affected community composition, albeit in different ways. Development significantly increased species richness and exponential Shannon diversity, while invasion had no effect on these variables. However, invasion significantly increased arthropod abundance and caused biotic homogenization. Specifically, uninvaded arthropod communities were distinctly different in species composition between developed and natural sites, while they became undistinguishable after A. leptopus invasion. Moreover, functional variables were significantly affected by species invasion, but not by urban development. Invaded communities had higher community‐weighted mean body size and the feeding guild composition of invaded arthropod communities was characterized by the exceptional numbers of nectarivores, herbivores, and detritivores. With the exception of species richness and exponential Shannon diversity, invasion influenced four out of six response variables to a greater degree than urban development did. Hence, we can conclude that species invasion is not just a passenger of urban development but also a driver of change.     

Nonrandom co-occurrence patterns of rainforest chameleons

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

Disentangling the effects of geographic distance and environmental dissimilarity on global patterns of species turnover

Aim To distinguish the effects of geographic distance and environmental dissimilarity on global patterns of species turnover in four classes of terrestrial vertebrates (mammals, birds, reptiles and amphibians). Location Six hundred and sixty terrestrial ecoregions across the globe. Methods We calculated species turnover between each pair of ecoregions, using the Jaccard index (J). We selected seven variables to quantify environment in each ecoregion, and subjected the environmental values to a principal components analysis. For each realm, we applied multiple regression analysis relating the natural logarithm of the Jaccard index (lnJ) to geographic distance alone and in combination with differences in the environment variables measured as principal components (PC). We used partial correlations to partition variance in lnJ between unique contributions of distance and environmental PC scores, the covariation between distance and environment, and unexplained variance. To examine the latitude and species turnover relationship, we regressed lnJ on latitude with distance between ecoregions being included as a covariate. Results The natural logarithm of the Jaccard index (lnJ) decreased significantly with increasing geographic distance for all vertebrate classes in each zoogeographic realm, and the slopes of the relationships per 1000 km ranged from ?0.251 to ?1.043. With environmental differences included in the analysis, both geographic distance and environmental differences were substantial predictors of lnJ for every combination of taxon and realm. On average, the unique contribution of geographic distance to variation in species turnover between ecoregions was about 1.4 times that of the environmental differences between ecoregions. Species turnover generally decreased with increasing latitude when controlling for geographic distance. The value of lnJ for each vertebrate class was highly and positively correlated with those of the other vertebrate classes. Main conclusions Our analyses suggest that both dispersal‐based and niche‐based processes have played important roles in determining faunal similarities among vertebrate assemblages at the spatial scale examined. Furthermore, reptiles and amphibians exhibited greater distance‐independent faunal heterogeneity among ecoregions and greater turnover among ecoregions with respect to geographic and environmental distance than birds and mammals.     

Abundance and co-occurrence patterns of core and satellite species of ground beetles on small lake islands

15 lake islands and two mainland sites of Mamry lake in Poland were sampled to investigate community structures and patterns of co-occurrences of ground beetles (Carabidae). The total ground beetle metacommunity of 71 species was divided into a group of core species occupying at least half of all study sites and of satellite species, which occurred at two sites or less. This division is mirrored by reduced dispersal abilities and non-random patterns of site occupancy. Core and satellite species also differed in patterns of relative abundance. The core group followed a lognormal distribution, the satellite group a power function as predicted by the self-similarity model of occurrence. We conclude that the division into core and satellite species is not a sample artefact but reflects different life history strategies. We also conclude that current models of niche division and co-occurrence might miss important aspects of community structure if they do not refer to patterns of dispersal.
From these findings we infer that the regional distribution of core species might be shaped by species interactions and processes of niche divisions whereas the spatial distribution of satellite species are best interpreted as stemming from random dispersal.     

On the meaning and measurement of nestedness of species assemblages

Nestedness of species assemblages occurs when thebiotas of sites with lower numbers of species tend to be subsets of the biotas at richer sites. We develop new quantitative and statistical techniques for measuring, testing, and comparing nestedness, and apply these methods to data from the literature. Significantly nonrandom nestedness was present in all 27 assemblages examined, and tended to be stronger in systems dominated by extinction, such as landbridge islands. Sets of assemblages that were very strongly nested were more likely to have greater species richness on one or a few large sites than on several smaller sites of equivalent total area — that is, to fall toward the single large side of the Single Large Or Several Small (SLOSS) continuum. Our analysis indicates that nestedness, when quantified as a single number for a presence-absence matrix, measures community-wide differences in incidence (the frequency of occurrence or distribution of species). Factors that lead to consistent differences among species in immigration or extinction rates cause strong patterns of nestedness of species assemblages. Nestedness is negatively related to beta diversity: nestedness is low when beta diversity is high, and vice versa. Conservation managers will thus seek to minimize nestedness and the development of nested structure in systems of nature reserves.     

A metacommmunity approach to co-occurrence patterns and the core-satellite hypothesis in a community of tropical arboreal ants

Inferring mechanisms of community assembly from co-occurrence patterns is difficult in systems where assembly processes occur at multiple spatial scales and among species with heterogeneous dispersal abilities. Here, we demonstrate that local scale analysis of co-occurrence patterns is inadequate to fully describe assembly mechanisms and instead utilize a metacommunity and core-satellite approach. We generated a co-occurrence and life-history data set for a community of twig-nesting ants on coffee plants across 36 sites within a tropical agroecosystem to test the following three hypotheses: (1) twig-nesting ant species compete for nest-sites, (2) they are structured as a metacommunity, and (3) core species show segregated patterns, while satellite species show random patterns of co-occurrence. Species were divided into four groups: core species that are well distributed regionally and dominant locally, regional dominants that are well distributed regionally but do not dominate locally, local dominants that are dominant locally but are not widely distributed, and satellites that are neither widely distributed nor dominant locally. Only the most abundant species in the community, Pseudomyrmex simplex, was classified as a core species. Regional dominants, local dominants, and satellite species show random patterns of co-occurrence. However, when P. simplex is included in the co-occurrence matrix, patterns become aggregated for all three species groupings. This suggests that P. simplex “assembles” the community by providing a core metapopulation that other species track. Analyzing co-occurrence patterns among candidate subsets of species, at multiple spatial scales, and linking them to species traits substantially improves the explanatory power of co-occurrence analyses in complex metacommunities.     

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.