Phylogeny and co‐occurrence of mammal species on Southeast Asian islands

Aim Islands have often been used as model systems in community ecology. The incorporation of information on phylogenetic relatedness of species in studies of island assemblage structure is still uncommon, but could provide valuable insights into the processes of island community assembly. We propose six models of island community assembly that make different predictions about the associations between co‐occurrences of species pairs on islands, phylogenetic relatedness and ecological similarity. We then test these models using data on mammals of Southeast Asian islands. Location Two hundred and forty islands of the Sundaland region of Southeast Asia. Methods We quantified the co‐occurrence of species pairs on islands, and identified pairs that co‐occur more frequently (positive co‐occurrence) or less frequently (negative co‐occurrence) than expected under null models. We then examined the distributions of these significantly deviating pairs with respect to phylogenetic relatedness and ecological differentiation, and compared these patterns with those predicted by the six community assembly models. We used permutation regression to test whether co‐occurrence patterns are predicted by relatedness, body size difference or difference in diet quality. Separate co‐occurrence matrices were analysed in this way for seven mammal families and four smaller subsets of the islands of Sundaland. Results In many matrices, average numbers of negative co‐occurrences were higher than expected under null models. This is consistent with assemblage structuring by competition, but may also result from low geographic overlap of species pairs, which contributes to negative co‐occurrences at the archipelago‐wide level. Distributions of species pairs within plots of phylogenetic distance × ecological differentiation were consistent with competition, habitat filtering or within‐island speciation models, depending on the taxon. Regressions indicated that co‐occurrence was more likely among closely related species pairs within the Viverridae and Sciuridae, but in most matrices phylogenetic distance was unrelated to co‐occurrence. Main conclusions Simple deterministic models linking co‐occurrence with phylogeny and ecology are a useful framework for interpreting distributions and assemblage structure of island species. However, island assemblages in Sundaland have probably been shaped by a complex idiosyncratic set of interacting ecological and evolutionary processes, limiting the predictive power of such models.     

Aggregative structure is the rule in communities of fleas: null model analysis

We used null models to examine patterns of species co‐occurrences in 59 communities of fleas parasitic on small mammals from 4 biogeographic realms (Afrotropics, Nearctic, Neotropics, and Palaearctic). We compared frequencies of co‐occurrences of flea species across host species with those expected by chance, using a null model approach. We used 4 tests for non‐randomness to identify pairs of species (within a community) that demonstrate significant positive or negative co‐occurrence. The majority of flea communities were non‐randomly assembled. Patterns of flea co‐occurrences on the same host species indicated aggregation but not segregation of flea species (except for the flea community of Madagascar). Although only a small fraction of species pairs were associated significantly (264 of 10, 943 species pairs according to the most liberal criterion), most of these associations were positive (except for 2 negatively associated species pairs). Significantly associated pairs were represented mainly by non‐congeneric species. The degree of non‐randomness of the entire flea community was similar among biogeographic regions, but the strength of pair‐wise association varied geographically, being the highest in the Afrotropics and the lowest in the European region of the Palaearctic.     

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.     

Binary matrices and checkerboard distributions of birds in the Bismarck Archipelago

Aim We examine a presence–absence matrix of the avifauna of the Bismarck Archipelago, for which the concept of competitively driven community assembly rules was formulated, to determine whether data support widespread competitive determination of geographical distributions. Location Bismarck Archipelago. Methods We obtained occurrences of 154 land and freshwater bird species on 31 islands. We calculated the observed number of checkerboards for all species pairs, for congeneric species pairs and for pairs of species within guilds, and employed randomization techniques to detect unusual co‐occurrence patterns. Results Compared with random expectations, there are excesses of checkerboard pairs within both genera and defined guilds, but a detailed examination shows that competition is a cogent possible explanation in few instances. For many checkerboard pairs, species are not widely interspersed but are regionally allopatric, which probably reflects historical biogeography and dispersal limitation. Most congeneric and intraguild checkerboards include a species classified as a supertramp; when supertramps are omitted, there are 11 congeneric checkerboards and four intraguild but heterogeneric checkerboards. Main conclusions In isolation, presence–absence matrices provide limited insight into the role of competition in structuring bird communities of the Bismarcks. A major problem is disentangling historical geography and colonization history of the archipelago from the present‐day ecology of the species. Examination of observed checkerboards from a geographically explicit perspective and with knowledge of colonization routes suggests that many checkerboards are likely to result, at least in part, from historical biogeography and supertramps. Although species may be forced into supertramp status by competition, other factors (e.g. habitat preference) may be causal, and biogeographical distributions alone cannot distinguish between causes.     

Taxonomic relatedness and spatial structure of a shelf benthic gastropod assemblage

Aim Phylogenetically related species share attributes that lead to common responses to environmental conditions, but which could also produce the exclusion of species by its relatives. These processes could generate the patterns of phylogenetic attraction or repulsion in local communities, where related species would tend to coexist more or less than expected by chance. This paper aims to (1) analyse the phylogenetic structure of a benthic gastropod assemblage in the south‐western Atlantic Ocean (SAO); (2) explore the linkages between phylogenetic structure and spatial distribution patterns; (3) compare outcomes driven by the analysis of presence‐only data and predictive species distribution models; and (4) explore which aspects of the gained knowledge can be useful to the design of sound conservation and/or management actions. Location Uruguayan shelf and slope in the SAO. Methods Spatial patterns in taxonomical relatedness were assessed using (1) raw presence/absence data (i.e. realized niche approach) and (2) reconstruction of the potential composition of the assemblage from niche modelling (i.e. fundamental niche approach). Null models were used to test hypotheses on assemblage structure. Results Significant departures from the null hypothesis that all species were drawn from the same assemblage were observed irrespectively of the approach, indicating the existence of non‐random structures. However, a high proportion of local communities can be thought as random subsets of the regional species pool. This lack of a strong signal of a taxonomic effect could be related to the absence of a linkage between taxonomic distances and ecological similarities. Main conclusions Our results suggest a random assembly of local communities from the regional species pool and/or niche filtering independent of phylogeny as main determinants of local community composition. We also suggest that local assemblages displaying significantly higher (or lower) than expected taxonomic relatedness should be taken into consideration for designing spatially explicit conservation measures.     

Coexistence patterns of benthic gastropods on the Uruguayan shelf

Community assembly rules theory attempt to understand the processes that determine the composition of local communities from a regional species pool. Nestedness and negative co‐occurrence are two of the most commonly reported meta‐community patterns, but almost exclusively from terrestrial and freshwater ecosystems. Here we analyzed the structure of species coexistence in six datasets containing presence/absence data for 120 marine benthic gastropod species in 249 sampling units on the Uruguayan continental shelf and Río de la Plata estuary. The ecological features of this system, such as the idiosyncratic nature of the biogeographic and oceanographic realms, are clearly different from those observed in other systems previously targeted by studies on coexistence structure. Community patterns were evaluated using null models and four structure indices. The existence of patterns in community assembly, and in particular segregated co‐occurrence, was verified only when analyzing the number of checkerboard units (CH index). This indicates more mutually exclusive species pairs than expected by chance. Nestedness, on the other hand, was not detected in any dataset. Storage and rescue effects related to overall high immigration and low local extinction rates are plausible mechanisms to account for the general pattern of random species coexistence, while the segregated co‐occurrence pattern depicted by the CH index may be related to differential habitat requirements within species pairs. Our study highlights the importance of analyzing metacommunity structures in alternative biological, environmental, and historical contexts in order to advance on the construction of a general ecological theory, relating patterns with the processes dominating in particular ecosystems.     

A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities

Trait‐based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat‐specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat‐specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co‐occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine‐scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.     

Fire disturbance disrupts co‐occurrence patterns of terrestrial vertebrates in Mediterranean woodlands

Aim This paper uses null model analysis to explore the pattern of species co‐occurrence of terrestrial vertebrate fauna in fire‐prone, mixed evergreen oak woodlands. Location The Erico–Quercion ilicis of the Mediterranean belt (50–800 m a.s.l.) in the Madonie mountain range, a regional park in northern Sicily (37°50′ N, 14°05′ E), Italy. Methods The stratified sampling of vertebrates in a secondary succession of recent burned areas (BA, 1–2 years old), intermediate burned areas (INT, 4–10 years old) and ancient burned areas (CNB, > 50 years old), plus forest fragments left within burned areas (FF, 1–2 years old) permitted the comparison of patterns of species co‐occurrence using a set of separate presence/absence matrices. First, the breeding avifauna derived from standardized point counts was analysed using Stone & Roberts’C‐score, and by a null model algorithm (fixed/equiprobable). Secondly, the analysis was repeated using all vertebrate species recorded in the succession. Results Sixty‐five species were recorded in the 2‐year study period in the four sample treatments. Birds were found to make up the largest component (63%) of the recorded assemblage. The BA treatment had the lowest species richness, followed in order by the small, medium and large FFs, and then by the CNBs. For both analyses (birds and total vertebrates), the C‐scores were quite small and not significantly different from those that could be expected by chance in the BA and INT burned areas; this indicates a random co‐occurrence among vertebrates of those assemblages. Contrariwise, for both analyses in the CNBs, the C‐scores were large and significantly different from the simulated indices, thereby indicating a non‐random co‐occurrence pattern (segregation) of vertebrates in the undisturbed woodlands. In addition, C‐score values for the surviving FFs show a significant aggregation of species. Main conclusions The null model analyses highlighted a new aspect of fire disturbance in Mediterranean woodland ecosystems: the disruption in patterns of co‐occurrence in the terrestrial vertebrate community. Wildfire alters community organization, inducing, for at least 10 years, a random aggregate of species. Communities re‐assemble themselves, showing the occurrence of species segregation at least 50 years after fire.     

Fine-scale structure and cross-taxon congruence of bird and beetle assemblages in an old-growth boreal forest mosaic

Aim Nestedness occurs when species present in depauperate sites are subsets of those found in species‐rich sites. The degree of congruence of site nestedness among different assemblages can inform commonalities of mechanisms structuring the assemblages. Well‐nested assemblages may still contain idiosyncratic species and sites that notably depart from the typical assemblage pattern. Idiosyncrasy can arise from multiple processes, including interspecific interactions and habitat preferences, which entail different consequences for species co‐occurrences. We investigate the influence of fine‐scale habitat variation on nestedness and idiosyncrasy patterns of beetle and bird assemblages. We examine community‐level and pairwise species co‐occurrence patterns, and highlight the potential influence of interspecific interactions for assemblage structure. Location Côte‐Nord region of Québec, Canada. Methods We sampled occurrences of ground‐dwelling beetles, flying beetles and birds at sites within old‐growth boreal forest. We examined the nestedness and idiosyncrasy of sites and sought relationships to habitat attributes. We analysed non‐random species co‐occurrence patterns at pairwise and community levels, using null model analysis and five ‘association’ indices. Results All three assemblages were significantly nested. There was limited congruence only between birds and flying beetles whose nestedness was related to canopy openness. For ground‐dwelling beetles, nestedness was related to high stand heterogeneity and sapling density, whereas site idiosyncrasy was inversely related to structural heterogeneity. For birds, site idiosyncrasy increased with canopy cover, and most idiosyncratic species were closed‐canopy specialists. In all assemblages, species idiosyncrasy was positively correlated with the frequency of negative pairwise associations. Species co‐occurrence patterns were non‐random, and for flying beetles and birds positive species pairwise associations dominated. Community‐level co‐occurrence summaries may not, however, always reflect these patterns. Main conclusions Nestedness patterns of different assemblages may not correlate, even when sampled at common locations, because of different responses to local habitat attributes. We found idiosyncrasy patterns indicating opposing habitat preferences, consistent with antagonistic interactions among species within assemblages. Analysis of such patterns can thus suggest the mechanisms generating assemblage structures, with implications for biodiversity conservation.     

Are soil lichen communities structured by biotic interactions? A null model analysis

Question: Are soil lichen communities structured by biotic interactions? Location: Gypsum outcrops located next to Belmonte del Tajo, central Spain. Methods: We sampled a total of 68 (50 cm × 50 cm) plots in gypsum outcrops from central Spain. Each plot was divided into 100 (5 cm × 5 cm) sampling quadrats, and the presence of all lichen species in every quadrat was recorded (6800 quadrats in total). We used two realistic null models to generate random communities unstructured by biotic interactions, and used them to test the hypothesis that soil lichen species co‐occur less often than expected by chance. Results: We found fewer species combinations and less co‐occurrence than expected by chance. However, the latter result was dependent on the null model selected. The number of checkerboard pairs did not differ significantly from the null expectation. Conclusions: Overall, our results suggest that gypsiferous soil lichen communities are structured by competitive interactions. They are consistent with studies conducted with a wide variety of taxa, and fill a gap in our knowledge of the factors driving the small‐scale distribution of these important organisms.     

The immediate and long‐term effects of water drawdown on macrophyte assemblages in a large subtropical reservoir

1. Disturbances play a central role in determining the spatial and temporal dynamics of many plant communities. In our study of macrophyte assemblages at 150 sites in five arms of a large subtropical reservoir (Itaipu Reservoir, Brazil–Paraguay border), we used co‐occurrence null models and spatiotemporal analyses to describe the patterns in the assemblages during a historically large water drawdown in 2000, in comparison with the previous year (1999) and subsequent years (2001–07). A C‐Score co‐occurrence index tested the null hypothesis of random structure during the drawdown period. A detrended correspondence analysis and multiresponse permutation procedure were used to verify whether species composition differed before, during and after the disturbance. 2. In contrast to our expectations, the null models showed that the macrophyte assemblages were spatially structured during the drawdown (2000), although species composition was significantly different from the previous year (1999) and also changed in the following years (2001–07). Significant species co‐occurrence patterns were generated by the drawdown disturbance, with species extinctions and colonisation by new species from propagules and seed bank germination. 3. The randomness we expected in 2000 actually occurred in 2001, probably because the reestablishment of normal water level enabled both submersed and free‐floating species to recolonise the shore that emergent species had inhabited since the drawdown. Biotic interactions appeared to increase during the years after the disturbance and the habitat preferences of the aquatic macrophytes were re‐established, resulting in higher similarities in aquatic macrophyte species composition in the years after the drawdown.     

How do similarities in spatial distributions and interspecific associations affect the coexistence of Quercus species in the Baotianman National Nature Reserve,Henan, China

Congeneric species often have similar ecological characteristics and use similar resources. These similarities may make it easier for them to co‐occur in a similar habitat but may also lead to strong competitions that limit their coexistence. Hence, how do similarities in congeneric species affect their coexistence exactly? This study mainly used spatial point pattern analysis in two 1 hm² plots in the Baotianman National Nature Reserve, Henan, China, to compare the similarities in spatial distributions and interspecific associations of Quercus species. Results revealed that Quercus species were all aggregated under the complete spatial randomness null model, and aggregations were weaker under the heterogeneous Poisson process null model in each plot. The interspecific associations of Quercus species to non‐Quercus species were very similar in Plot 1. However, they can be either positive or negative in different plots between the co‐occurring Quercus species. The spatial distributions of congeneric species, interspecific associations with non‐Quercus species, neighborhood richness around species, and species diversity were all different between the two plots. We found that congeneric species did have some similarities, and the closely related congeneric species can positive or negative associate with each other in different plots. The co‐occurring congeneric species may have different survival strategies in different habitats. On the one hand, competition among congenerics may lead to differentiation in resource utilization. On the other hand, their similar interspecific associations can strengthen their competitive ability and promote local exclusion to noncongeneric species to obtain more living space. Our results provide new knowledge for us to better understand the coexistence mechanisms of species.     

Species richness correlates of raw and standardized co‐occurrence metrics

Measuring β‐diversity and changes in species composition across multiple sites and environments is a major research focus in macroecology, and a variety of metrics have been proposed to quantify species co‐occurrence patterns in a species × site occurrence matrix. However, indices of β‐diversity and species co‐occurrence are often statistically dependent on the number of species in an assemblage. We compared the results of several common co‐occurrence metrics with patterns generated by a spatially explicit neutral model simulation. We found that all measures of co‐occurrence and β‐diversity, whether raw, rescaled or standardized by a null model expectation, were highly correlated with the total species richness of the landscape. The one important exception were the effect sizes of the fixed–fixed null model algorithm, which preserves row and column sums of the original matrix during matrix randomization. Our results call for a careful interpretation of meta‐analyses of assemblages that differ widely in species richness. At a minimum, observed species richness should be used as a statistical covariate in regression analyses, and results of the fixed–fixed algorithm should be compared carefully with the results of other randomization tests.     

Interspecific aggregation of ectoparasites on bats: importance of hosts as habitats supersedes interspecific interactions

Patterns of aggregation of species or individuals may result from combinations of interspecific interactions such as competition, facilitation, or apparent facilitation, as well as from equivalent responses to environmental factors. Host–parasite systems are ideal for the investigation of mechanisms that structure assemblages. Interspecific aggregation is documented for multiple groups that are ectoparasitic on mammals and host‐mediated apparent facilitation has been suggested to explain these aggregation patterns. To investigate the generality of this pattern and to determine likely structuring mechanisms, I analyzed species co‐occurrence, correlations of abundances, and nestedness for ectoparasite assemblages from each of 11 species of Neotropical bat. Ectoparasite assemblages on four of 11 host species exhibited significant positive co‐occurrence for the entire assemblage or for at least one pair of species in the assemblage; ectoparasites on two host species exhibited positive co‐occurrence that approached significance. There was no evidence of negative co‐occurrence. Nine species‐pairs exhibited positive abundance correlations, including seven of the eight species‐pairs that exhibited positive co‐occurrence. No species‐pair exhibited a negative correlation of abundances (i.e. density compensation). Ectoparasite assemblages from five of 11 host species exhibited nestedness, including all three assemblages that exhibited assemblage‐wide positive co‐occurrence. Multiple mechanisms associated with host characteristics may contribute to host aggregation in ectoparasite assemblages, including host body size, vagility, home range size, burrow or roost size and complexity, immunocompetence and social structure. In general, data in this study and elsewhere are not consistent with interspecific interactions among ectoparasites, including apparent facilitation, being primary structuring mechanisms of ectoparasite assemblages on mammalian hosts. Rather, host behavior and ecology are likely to affect the frequency of host–ectoparasite encounters and of conspecific host interactions that facilitate transfer of ectoparasites, thereby, molding patterns of ectoparasite co‐occurrence, abundance and species composition on mammalian hosts. Combinations of characteristics that are primarily responsible for molding ectoparasite assemblage composition likely are host‐taxon specific.     

The diversity field of New World leaf‐nosed bats (Phyllostomidae)

Aim To analyse how the patterns of species richness for the whole family Phyllostomidae determine the structure of diversity fields (sets of species‐richness values) within the ranges of individual bat species. Location The range of the family Phyllostomidae in North and South America. Methods We generated a database of the occurrence of 143 phyllostomid bat species in 6794 quadrats, analysing the species‐richness frequency distribution for all sites, and for subsets of sites defined by the geographic ranges of species. Range–diversity plots, depicting simultaneously the size and the mean species richness of ranges, were built to explore the patterns of co‐occurrence in widespread and restricted species. We compared the empirical patterns against two null models: (1) with scattered (non‐cohesive) ranges, and (2) with cohesive ranges modelled with the spreading‐dye algorithm. Diversity fields were analysed with richness maps for individual species and with comparisons of species‐richness frequency distributions. Results Overall richness frequency distribution showed a multimodal pattern, whereas simulated distributions showed lower values of variance, and were unimodal (for model 1) and bimodal (for model 2). Range–diversity plots for the empirical data and for the cohesive‐ranges simulation showed a strong tendency of species to co‐occur in high‐diversity sites. The scattered‐ranges simulation showed no such tendency. Diversity fields varied according to idiosyncratic features of species generating particular geographic patterns and richness frequency distributions. Main conclusions Phyllostomid bats show a higher level of co‐occurrence than expected from null models. That tendency in turn implies a higher variance in species richness among sites, generating a wider species‐richness frequency distribution. The diversity field of individual species results from the size, shape and location of ranges, but also depends on the general pattern of richness for the whole family.     

Pattern detection in null model analysis

Synthesis The identification of distinctive patterns in species x site presence‐absence matrices is important for understanding meta‐community organisation. We compared the performance of a suite of null models and metrics that have been proposed to measure patterns of segregation, aggregation, nestedness, coherence, and species turnover. We found that any matrix with segregated species pairs can be re‐ordered to highlight aggregated pairs, indicating that these seemingly opposite patterns are closely related. Recently proposed classification schemes failed to correctly classify realistic matrices that included multiple co‐occurrence structures. We propose using a combination of metrics and decomposing matrix‐wide patterns into those of individual pairs of species and sites to pinpoint sources of non‐randomness. Null model analysis has been a popular tool for detecting pattern in binary presence–absence matrices, and previous tests have identified algorithms and metrics that have good statistical properties. However, the behavior of different metrics is often correlated, making it difficult to distinguish different patterns. We compared the performance of a suite of null models and metrics that have been proposed to measure patterns of segregation, aggregation, nestedness, coherence, and species turnover. We found that any matrix with segregated species pairs can be re‐ordered to highlight aggregated pairs. As a consequence, the same null model can identify a single matrix as being simultaneously aggregated, segregated or nested. These results cast doubt on previous conclusions of matrix‐wide species segregation based on the C‐score and the fixed‐fixed algorithm. Similarly, we found that recently proposed classification schemes based on patterns of coherence, nestedness, and segregation and aggregation cannot be uniquely distinguished using proposed metrics and null model algorithms. It may be necessary to use a combination of different metrics and to decompose matrix‐wide patterns into those of individual pairs of species or pairs of sites to pinpoint the sources of non‐randomness.     

Body size and coexistence in gamasid mites parasitic on small mammals: null model analyses at three hierarchical scales

We studied body size ratio in gamasid mites (Acari: Mesostigmata) parasitic on Palearctic small mammals at 3 hierarchical scales, namely infracommunities (an assemblage of mites harboured by an individual host), component communities (an assemblage of mites harboured by a host population), and compound communities (an assemblage of mites harboured by a host community). We used null models and asked a) whether body size distributions in these communities demonstrate non‐random patterns; b) whether these patterns indicate segregation or aggregation of body sizes of coexisting species; and c) whether patterns of body size distribution are scale‐dependent, that is, differ among infracommunities, component communities, and compound communities. In most mite assemblages, the observed pattern of body size distribution did not differ from that expected by chance. However, meta‐analyses demonstrated that component and compound communities of gamasid mites consistently demonstrated a tendency to reduced body size overlap, while we did not find any clear trend in mite body size distribution across infracommunities. We discuss reasons for scale‐dependence of body size distribution pattern in parasite communities and propose ecological and evolutionary mechanisms that allowed the reduced body size overlap in component and compound communities of ectoparasites to arise.     

Using null model analysis of species co-occurrences to deconstruct biodiversity patterns and select indicator species

Aim Using total species richness to characterize biodiversity may mask multiple response patterns of species. We propose a null model analysis of species co‐occurrence‐based classification to identify sets of species that may have similar (within‐groups) and distinct (between groups) response patterns to their environment. The classification should also provide an explicit framework for selecting indicator species with characteristic co‐occurrence patterns to predict overall species richness. Location Côte‐Nord, Québec, Canada. Methods We combined null‐model of species co‐occurrence and cluster analysis to identify species groups within diverse assemblages of ground‐dwelling and flying beetles of stands in a boreal forest mosaic; we then examined their co‐occurrence and response patterns to habitat characteristics. Best subset regressions were used to select indicator species of richness within each group, from which indicators of total species richness were selected. Results The identified species groups appeared to display contrasting co‐occurrence and response patterns to at least one of the stand‐level habitat characteristics. Among flying beetles, for example, richness increased with stand‐level heterogeneity for two groups and decreased for two other groups, but the relationship was non‐significant for the total richness. We identified 28 indicator species that explained > 80% (validated by bootstrap analysis) of the variation in total species richness. Predictive performance of indicators was higher than when their co‐occurrence were reshuffled, even under a highly constrained null model, indicating that co‐occurrence patterns contributed to their predictive performance. Main conclusions Co‐occurrence‐based classification appears as a promising and effective tool for deconstructing biodiversity into species groups which reflect their ecological commonalities and differences, thus reducing the risk of making faulty inferences about the causes underlying overall diversity patterns. The method provides an explicit framework for selecting indicator species representing different species groups that may reflect the multiple responses of species co‐occurring with them. Indicator species can be effective for predicting overall species richness.     

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).     

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

Co‐occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co‐existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co‐occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co‐occurrence networks to identify pairs of significantly associated taxa, either co‐existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat‐filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co‐occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.