The net effects of interspecific species interactions on individuals and populations vary in both sign (À, 0, +) and magnitude (strong to weak). Interaction outcomes are context-dependent when the sign and/or magnitude change as a function of the biotic or abiotic context. While context dependency appears to be common, its distribution in nature is poorly described. Here, we used meta-analysis to quantify variation in species interaction outcomes (competition, mutualism, or predation) for 247 published articles. Contrary to our expectations, variation in the magnitude of effect sizes did not differ among species interactions, and while mutualism was most likely to change sign across contexts (and predation least likely), mutualism did not strongly differ from competition. Both the magnitude and sign of species interactions varied the most along spatial and abiotic gradients, and least as a function of the presence/absence of a third species. However, the degree of context dependency across these context types was not consistent among mutualism, competition and predation studies. Surprisingly, study location and ecosystem type varied in the degree of context dependency, with laboratory studies showing the highest variation in outcomes. We urge that studying context dependency per se, rather than focusing only on mean outcomes, can provide a general method for describing patterns of variation in nature.

All species are hierarchically related to one another, and we use taxonomic names to label the nodes in this hierarchy. Taxonomic data is becoming increasingly available on the web, but scientists need a way to access it in a programmatic fashion that’s easy and reproducible. We have developed taxize, an open-source software package (freely available from http://cran.r-project.org/web/packages/taxize/index.html) for the R language. taxize provides simple, programmatic access to taxonomic data for 13 data sources around the web. We discuss the need for a taxonomic toolbelt in R, and outline a suite of use cases for which taxize is ideally suited (including a full workflow as an appendix). The taxize package facilitates open and reproducible science by allowing taxonomic data collection to be done in the open-source R platform.

Context dependency, variation in the outcome of species interactions with biotic and abiotic conditions, is increasingly considered ubiquitous among mutualisms. Despite several qualitative reviews of many individual empirical studies, there has been little quantitative synthesis examining the generality of context dependency, or conditions that may promote it. We conducted a meta‐analysis of ant–plant protection mutualisms to examine the generality of context‐dependent effects of ants on herbivory and plant performance (growth, reproduction). Our results show that ant effects on plants are not generally context dependent, but instead are routinely positive and rarely neutral, as overall effect sizes of ants in reducing herbivory and increasing plant performance were positive and significantly greater than 0. The magnitude of these positive effects did vary, however. Variation in plant performance was not explained by the type of biotic or abiotic factor examined, including plant rewards (extrafloral nectar, food bodies, domatia), ant species richness, plant growth form, or latitude. With the exception of plant growth form, these factors did contribute to the effects of ants in reducing herbivory. Reductions in herbivory were greater for plants with than without domatia, and greatest for plants with both domatia and food bodies. Effect sizes of ants in reducing herbivory decreased, but remained positive, with latitude and ant species richness. Effect sizes in reducing herbivory were greater in tropical vs. temperate systems. Although ant–plant interactions have been pivotal in the study of context dependency of mutualisms, our results, along with other recent meta‐analyses, indicate that context dependency may not be a general feature of mutualistic interactions. Rather, ant–plant protection mutualisms appear to be routinely positive for plants, and only occasionally neutral.

Meta‐analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non‐independence exists among taxa, violating the statistical assumptions underlying traditional meta‐analytic models. Recently, meta‐analytical techniques incorporating phylogenetic information have been developed to address this issue. However, no syntheses have evaluated how often including phylogenetic information changes meta‐analytic results. To address this gap, we built phylogenies for and re‐analysed 30 published meta‐analyses, comparing results for traditional vs. phylogenetic approaches and assessing which characteristics of phylogenies best explained changes in meta‐analytic results and relative model fit. Accounting for phylogeny significantly changed estimates of the overall pooled effect size in 47% of datasets for fixed‐effects analyses and 7% of datasets for random‐effects analyses. Accounting for phylogeny also changed whether those effect sizes were significantly different from zero in 23 and 40% of our datasets (for fixed‐ and random‐effects models, respectively). Across datasets, decreases in pooled effect size magnitudes after incorporating phylogenetic information were associated with larger phylogenies and those with stronger phylogenetic signal. We conclude that incorporating phylogenetic information in ecological meta‐analyses is important, and we provide practical recommendations for doing so.

Interspecific interactions are often mediated by the interplay between resource supply and consumer density. The supply of a resource and a consumer's density response to it may in turn yield context-dependent use of other resources. Such consumer-resource interactions occur not only for predator-prey and competitive interactions, but for mutualistic ones as well. For example, consumer-resource interactions between ants and extrafloral nectar (EFN) plants are often mutualistic, as EFN resources attract and reward ants which protect plants from herbivory. Yet, ants also commonly exploit floral resources, leading to antagonistic consumer-resource interactions by disrupting pollination and plant reproduction. EFN resources associated with mutualistic ant-plant interactions may also mediate antagonistic ant-flower interactions through the aggregative density response of ants on plants, which could either exacerbate ant-flower interactions or alternatively satiate and distract ants from floral resources. In this study, we examined how EFN resources mediate the density response of ants on senita cacti in the Sonoran Desert and their context-dependent use of floral resources. Removal of EFN resources reduced the aggregative density of ants on plants, both on hourly and daily time scales. Yet, the increased aggregative ant density on plants with EFN resources decreased rather than increased ant use of floral resources, including contacts with and time spent in flowers. Behavioral assays showed no confounding effect of floral deterrents on ant-flower interactions. Thus, ant use of floral resources depends on the supply of EFN resources, which mediates the potential for both mutualistic and antagonistic interactions by increasing the aggregative density of ants protecting plants, while concurrently distracting ants from floral resources. Nevertheless, only certain years and populations of study showed an increase in plant reproduction through herbivore protection or ant distraction from floral resources. Despite pronounced effects of EFN resources mediating the aggregative density of ants on plants and their context-dependent use of floral resources, consumer-resource interactions remained largely commensalistic.

Summary 1.Nearly all mutualisms entail the production of resources by one species that attract and reward the species with which it interacts. As such resource production could otherwise be allocated to growth or reproduction, mutualists are predicted to minimize these investment costs. Here, we employ optimal defence theory for plant secondary compounds to evaluate plant production of extrafloral nectar (EFN) resources to attract and reward ants for resistance against herbivores. 2. Through ant exclusion and artificial herbivory experiments, we examined investment in EFN by both buds and fruits of Pachycereus schottii (senita cacti) in the Sonoran Desert of North America. We tested predictions of optimal defence theory that plants invest more in high value parts (fruits) through constitutive EFN, less in low value parts (buds) through induced EFN, and that for a given plant part (buds or fruits), constitutive and induced EFN are negatively correlated. 3. Constitutive levels of EFN were greater in fruits than in buds. Only buds showed induced EFN production following artificial herbivory. Constitutive EFN scaled positively with fruit size but not bud size. Induced EFN was negatively correlated with constitutive EFN for fruits (but not buds), suggesting a potential trade-off in these two herbivore resistance traits. 4. These results indicate that P. schottii minimizes its costs by investing in induced EFN for buds and constitutive EFN for fruits. Moreover, by shifting from induced to constitutive EFN with the morphogenesis of buds to fruits, our results show that investment in EFN can change as a particular plant tissue increases from a lower to a higher value. 5. Synthesis . Indirect defence through EFN production is in accord with that of direct defence through plant secondary compounds, thereby supporting optimal defence theory as a general framework with which to evaluate the costs of producing resources (i.e. the defence) by plants, lycaenids and homopterans to attract and reward ants for their resistance against natural enemies in protection mutualisms.

Recent research has shown that many mutualistic communities display non-random structures. While our understanding of the structural properties of mutualistic communities continues to improve, we know little of the biological variables resulting in them. Mutualistic communities include those formed between ants and extrafloral (EF) nectar-bearing plants. In this study, we examined the contributions of plant and ant abundance, plant and ant size, and plant EF nectar resources to the network structures of nestedness and interaction frequency of ant-plant networks across five sites within one geographic locality in the Sonoran Desert. Interactions between ant and plant species were largely symmetric. That is, ant and plant species exerted nearly equivalent quantitative interaction effects on one another, as measured by their frequency of interaction. The mutualistic ant-plant networks also showed nested patterns of structure, in which there was a central core of generalist ant and plant species interacting with one another and few specialist-specialist interactions. Abundance and plant size and ant body size were the best predictors of symmetric interactions between plants and ants, as well as nestedness. Despite interactions in these communities being ultimately mediated by EF nectar resources, the number of EF nectaries had a relatively weak ability to explain variation in symmetric interactions and nestedness. These results suggest that different mechanisms may contribute to structure of bipartite networks. Moreover, our results for ant-plant mutualistic networks support the general importance of species abundances for the structure of species interactions within biological communities.

Summary 1.The complexity of ecological communities can often hinder understanding their structural features. With the recent application of network theory, the structure of previously neglected mutualistic communities has begun to be elucidated. 2. Mutualistic communities have now been shown to follow particular power distributions in their degree, that is, the number of species interactions per species. However, predictive variables of degree and other structures of mutualistic networks remain largely unexplored. 3. Here, we show that body size of ants is positively correlated with their degree in mutualistic networks comprised of ant interactions with extrafloral nectar (EFN) bearing plants in the Sonoran Desert. This pattern in body size and the number of plant species with which ants interact occurred among all eight sampled communities, a relationship which was not contingent upon phylogenetic history among ant species. 4. These results indicate that further study of body size in ant-plant and other mutualistic networks may yield promising insights into the processes influencing their structure. Moreover, the degree-body size relationship for ant-plant mutualistic communities is consistent with that of predator-prey food webs, possibly suggesting similar underlying processes at work.