Species co‐occurrence patterns and dietary resource competition in primates

Diamond (Assembly of species communities. In: Cody ML, Diamond JM, editors. Ecology and evolution of communities. Cambridge: Belknap. p 342–444 ( 1975 )) argued that interspecific competition between species occupying similar niches results in a nonrandom pattern of species distributions. In particular, some species pairs may never be found in the same community due to competitive exclusion. Rigorous analytical methods have been developed to investigate the possible role that interspecific competition has on the evolution of communities. Many studies that have implemented these methods have shown support for Diamond's assembly rules, yet there are numerous exceptions. We build on this previous research by examining the co‐occurrence patterns of primate species in 109 communities from across the world. We used EcoSim to calculate a checkerboard (C) score for each region. The C score provides a measure of the proportion of species pairs that do not co‐occur in a set of communities. High C scores indicate that species are nonrandomly distributed throughout a region, and interspecific competition may be driving patterns of competitive exclusion. We conducted two sets of analyses. One included all primate species per region, and the second analysis assigned each species to one of four dietary guilds: frugivores, folivores, insectivores, and frugivore‐insectivores. Using all species per region, we found significantly high C scores in 9 of 10 regions examined. For frugivores, we found significantly high‐C scores in more than 50% of regions. In contrast, only 23% of regions exhibited significantly high‐C scores for folivores. Our results suggest that communities are nonrandomly structured and may be the result of greater levels of interspecific competition between frugivores compared to folivores. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Ecological correlates of the spatial co‐occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far‐reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co‐occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co‐occurrence. Within individual study areas, species pairs co‐occurred more frequently than expected at random. Co‐occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co‐occurrence decreased as compared to other species pairs when the pair included a large‐bodied carnivore. Our results suggest that a combination of shared traits and top‐down regulation by large carnivores shape local carnivore communities globally.     

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.     

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.     

Co‐occurrence is not evidence of ecological interactions

There is a rich amount of information in co‐occurrence (presence–absence) data that could be used to understand community assembly. This proposition first envisioned by Forbes (1907) and then Diamond (1975) prompted the development of numerous modelling approaches (e.g. null model analysis, co‐occurrence networks and, more recently, joint species distribution models). Both theory and experimental evidence support the idea that ecological interactions may affect co‐occurrence, but it remains unclear to what extent the signal of interaction can be captured in observational data. It is now time to step back from the statistical developments and critically assess whether co‐occurrence data are really a proxy for ecological interactions. In this paper, we present a series of arguments based on probability, sampling, food web and coexistence theories supporting that significant spatial associations between species (or lack thereof) is a poor proxy for ecological interactions. We discuss appropriate interpretations of co‐occurrence, along with potential avenues to extract as much information as possible from such data.     

Liana co‐occurrence patterns in a temperate rainforest

Questions: Are liana–host interactions structured at the community level? Do liana–host interactions differ between species, growth form guilds or habitats? Location: Otari‐Wilton's Bush, on the southern tip of North Island, New Zealand. The forest contains 75 ha of mature and regenerating conifer–broadleaf forest. Methods: Nine liana species were quantified among 217 trees to test for negative co‐occurrence patterns. We also conducted additional analyses within and among compartments embedded in the community‐level matrix. Liana and host abundance distributions were assessed across two contrasting habitats. Results: Community‐level analyses revealed negative co‐occurrence patterns. Positive, neutral and negative co‐occurrence patterns were found among compartments within the community‐level matrix. Host species compartments were consistent with randomized expectations, while positive co‐occurrence patterns were found within the host species matrix. Negative co‐occurrence patterns were found inconsistently among lianas that share the same region of host space, and those that do not. Conclusions: Overall, results indicate the liana community is structured non‐randomly. Liana–host interactions appear to follow an opportunistic growth strategy and interactions are due mostly to habitat partitioning.     

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.     

Species co‐occurrence analysis: pairwise versus matrix‐level approaches

Veech (2013, Global Ecology and Biogeography, 22 , 252–260) introduced a formula to calculate the probability of two species co‐occurring in various sites under the assumption of statistical independence between the two distributional patterns. He presented his model as a new procedure, a ‘pairwise approach’, different from analyses of whole presence–absence matrices to examine patterns of co‐occurrence. Here I show that: (1) Veech's method is identical to Fisher's exact test, a standard procedure for measuring the statistical association between two discrete variables; (2) in a broad sense, the pairwise approach is very similar to early analyses of spatial association, such as the one advanced by Forbes in 1907; (3) implicit in Veech's formula is a sampling scheme that is indistinguishable from well‐known matrix‐level null models that randomize the distribution of species among equiprobable sites; (4) pairwise co‐occurrence patterns can be analysed using any matrix‐level null model, so pairwise comparisons are not limited to using Veech's formula. The methodological distinction that Veech proposed between pairwise and matrix‐level approaches does not in fact exist, although the conceptual distinction between the two approaches is still a debated topic.     

Tree species composition and diversity in Miombo woodlands between co‐managed and government‐managed regimes,Malawi

Comparative information on the composition and diversity in tree species associations in Miombo woodland is limited. This study assessed how tree species associations across forest reserves of Miombo woodland in Malawi varied in composition and diversity concerning site factors and resource use disturbances under co‐management versus government management. Eighty nested circular plots, randomly selected in ArcGIS, were sampled to record stem diameter at breast height (DBH) of tree species: 0.04 ha for stems 5–29.9 cm DBH and 0.16 ha for stems ≥30 cm DBH. The recorded 109 tree species grouped into communities and 14 sub‐communities, using stem counts by species in TWINSPAN analysis. Sub‐divisions to level 5 showed eigenvalues ≥0.3, symbolising the stability of sub‐divisions. North/South sub‐divisions related to site factors; historical/current resource use influenced differences at levels 3–5. Species importance differed, indicating few important species in each sub‐community. Brachystegia and Julbernardia species showed importance across sub‐communities while Uapaca sansibarica in government management. Disturbances stimulated high species diversity. Recommendations include the need for a policy review towards group‐felling mature stands to stimulate regeneration and selective thinning of suppressed stems in stand development stages to maintain species diversity, productive recovery, diverse resource use value, and monitoring of harvesting impacts.     

The tangled link between β‐ and γ‐diversity: a Narcissus effect weakens statistical inferences in null model analyses of diversity patterns

Understanding the structure of and spatial variability in the species composition of ecological communities is at the heart of biogeography. In particular, there has been recent controversy about possible latitudinal trends in compositional heterogeneity across localities (β‐diversity). A gradient in the size of the regional species pool alone can be expected to impose a parallel gradient on β‐diversity, but whether β‐diversity also varies independently of the size of the species pool remains unclear. A recently suggested methodological approach to correct latitudinal β‐diversity gradients for the species pool effect is based on randomization null models that remove the effects of gradients in α‐ and γ‐diversity on β‐diversity. However, the randomization process imposes constraints on the variability of α‐diversity, which in turn force γ‐ and β‐diversity to become interdependent, such that any change in one is mirrored in the other. We argue that simple null model approaches are inadequate to discern whether correlations between α‐, β‐ and γ‐diversity reflect processes of ecological interest or merely differences in the size of the species pool among localities. We demonstrate that this kind of Narcissus effect may also apply to other metrics of spatial or phylogenetic species distribution. We highlight that Narcissus effects may lead to artificially high rejection rates for the focal pattern (Type II errors) and caution that these errors have not received sufficient attention in the ecological literature.     

Network analysis for co‐occurrence of pest insects on host crops

In this study, the co‐occurrence patterns of 618 pest insects for 47 host crops, including vegetables, grains, and fruits, were identified. To identify the pest co‐occurrence patterns for various crops, and the interactions among the pest insects and crops, we employed social network analysis methods. We used three traditional centrality measures (degree, closeness, and eigenvector) to determine the relative significance of each crop and pest as a node in the network. Throughout the network analysis, crops and pest nodes were divided into six groups, based on modularity. Crops in the same group could be considered as alternate hosts for pests from the same group. There were clear differences in the cultural practices between groups (i.e., dryland farming versus wetland farming). This indicated that dryland crop pests do not use wetland crops as resources. Pome fruit trees, such as apple and pear, had high centrality indices, which indicated the importance of these crops in the network and their high vulnerability to damage by a multitude of pests. In this study, although it was assumed that all crops were cultivated on the same piece of land during a single growing season, the complex interactions between the whole units were visualized and analyzed as a computable network.     

Habitat connectivity and dispersal ability drive the assembly mechanisms of macroinvertebrate communities in river networks

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Specific plasmid patterns and high rates of bacterial co‐occurrence within the coral holobiont

Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co‐occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad‐host‐range (BHR) plasmid groups, IncP‐1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co‐occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host‐specific bacteriome and co‐occurrence (and potential symbioses or niche space co‐dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host‐specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.     

Using fuzzy‐coded traits to elucidate the non‐random role of anthropogenic stress in the functional homogenisation of invertebrate assemblages

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Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history

Phylogenetic information is increasingly being used to understand the assembly of biological communities and ecological processes. However, commonly used metrics of phylogenetic diversity (PD) do not incorporate information on the relative abundances of individuals within a community. In this study, we develop three indices of PD that explicitly consider species abundances. First, we present a metric of phylogenetic-abundance evenness that evaluates the relationship between the abundance and the distribution of terminal branch lengths. Second, we calculate an index of hierarchical imbalance of abundances at the clade level encapsulating the distribution of individuals across the nodes in the phylogeny. Third, we develop an index of abundance-weighted evolutionary distinctiveness and generate an entropic index of phylogenetic diversity that captures both information on evolutionary distances and phylogenetic tree topology, and also serves as a basis to evaluate species conservation value. These metrics offer measures of phylogenetic diversity incorporating different community attributes. We compare these new metrics to existing ones, and use them to explore diversity patterns in a typical California annual grassland plant community at the Jasper Ridge biological preserve.
Ecology Letters (2010) 13: 96–105