Food webs are built up with nested subwebs

Global effects of land-use intensity and exotic plants on the structure and phylogenetic signal of plant-herbivore networks

Interactions between plants and herbivorous insects are often phylogenetically structured, with closely related insect species using similar sets of species or lineages of plants, while phylogenetically closer plants tend to share high proportions of their herbivore insect species. Notably, these phylogenetic constraints in plant-herbivore interactions tend to be more pronounced among internal plant-feeding herbivores (i.e., endophages) than among external feeders (i.e., exophages). In the context of growing human-induced habitat conversion and the global proliferation of exotic species, it is crucial to understand how ecological networks respond to land-use intensification and the increasing presence of exotic plants. In this study, we analyzed plant-herbivore network data from various locations of the World to ascertain the degree to which land-use intensity and the prevalence of exotic plants induce predictable changes in their network topology - measured by levels of nestedness and modularity - and phylogenetic structures. Additionally, we investigated whether the intimacy of plant-herbivore interactions, contrasting endophagous with exophagous networks, modulate changes in network structure. Our findings reveal that most plant-herbivore networks are characterized by significant phylogenetic and topological structures. However, neither these structures did not show consistent changes in response to increased levels of land-use intensify. On the other hand, for the networks composed of endophagous herbivores, the level of nestedness was higher in the presence of a high proportion of exotic plants. Additionally, for networks of exophagous herbivores, we observed an increase in the phylogenetic structure of interactions due to exotic host dominance. These results underscore the differential impacts of exotic species and land-use intensity on the phylogenetic and topological structures of plant-herbivore networks.

The Hierarchical Coevolutionary Units of Ecological Networks

In ecological networks, cohesive groups of species may shape the evolution of interactions, serving as coevolutionary units. Ranging across network scales, from motifs to isolated components, elucidating which cohesive groups are more determinant for coevolution remains a challenge in ecology. We address this challenge by integrating 376 empirical mutualistic and antagonistic networks and coevolutionary models. We identified cohesive groups at four network scales containing a significant proportion of potential direct coevolutionary effects. Cohesive groups displayed hierarchical organisation, and potential coevolutionary effects overflowing lower-scale groups were contained by higher-scale groups, underscoring the hierarchy's impact. However, indirect coevolutionary effects blurred group boundaries and hierarchy, particularly under strong selection from ecological interactions. Thus, under strong selection, indirect effects render networks themselves, and not cohesive groups, as the likely coevolutionary units of ecological systems. We hypothesise hierarchical cohesive groups to also shape how other forms of direct and indirect effects propagate in ecological systems.

The structure of bacteria-fungi bipartite networks along elevational gradients in contrasting climates

Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change.

Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.

Food webs reveal coexistence mechanisms and community organization in carnivores

Globally, massive carnivore guild extirpations have led to trophic downgrading and compromised ecosystem services. However, the complexity of multi-carnivore food webs complicates accurate identification of species interactions and community organization. Here, we used fecal DNA metabarcoding to investigate three communities that together encompass eight large- and meso-carnivore species and their 44 prey taxa of the Qinghai-Tibet Plateau (QTP), one of the last places on Earth that still harbors intact carnivore assemblages. Quantitative food-web analyses revealed pronounced interspecific variations in the carnivores' prey compositions and dietary partitioning both between and within guilds. Additionally, body masses of the carnivores and their prey exhibited consistent hump-shaped correlations across communities. Overall, differences in prey diversity, size category, and proportional utilization among the carnivore species result in trophic niche segregation that likely promotes carnivore coexistence in the harsh QTP environment. Network structure analyses detected significant modularity in all food webs but nestedness in only one. Furthermore, network characterization identified pikas (Ochotona spp.), bharal (Pseudois nayaur), and domestic yak (Bos grunniens) as potential keystone prey across the areas. Our results paint a holistic and detailed picture of the QTP carnivore assemblages' trophic networks and demonstrate that the combined use of the molecular dietary approach and network analysis can generate structural insights into carnivore coexistence and can identify functionally important species in complex communities. Such knowledge can help safeguard carnivore guild integrity and enhance community resilience to environmental perturbations in the sensitive QTP ecosystems.

Analysis of food chain mathematical model under fractal fractional Caputo derivative

In this article, the dynamical behavior of a complex food chain model under a fractal fractional Caputo (FFC) derivative is investigated. The dynamical population of the proposed model is categorized as prey populations, intermediate predators, and top predators. The top predators are subdivided into mature predators and immature predators. Using fixed point theory, we calculate the existence, uniqueness, and stability of the solution. We examined the possibility of obtaining new dynamical results with fractal-fractional derivatives in the Caputo sense and present the results for several non-integer orders. The fractional Adams-Bashforth iterative technique is used for an approximate solution of the proposed model. It is observed that the effects of the applied scheme are more valuable and can be implemented to study the dynamical behavior of many nonlinear mathematical models with a variety of fractional orders and fractal dimensions.

Complex Dynamic Behaviour of Food Web Model with Generalized Fractional Operator

We apply a new generalized Caputo operator to investigate the dynamical behaviour of the non-integer food web model (FWM). This dynamical model has three population species and is nonlinear. Three types of species are considered in this population: prey species, intermediate predators, and top predators, and the top predators are also divided into mature and immature predators. We calculated the uniqueness and existence of the solutions applying the fixed-point hypothesis. Our study examines the possibility of obtaining new dynamical phase portraits with the new generalized Caputo operator and demonstrates the portraits for several values of fractional order. A generalized predictor–corrector (P-C) approach is utilized in numerically solving this food web model. In the case of the nonlinear equations system, the effectiveness of the used scheme is highly evident and easy to implement. In addition, stability analysis was conducted for this numerical scheme.

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km² riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases and decreases towards downstream location within the catchment for fish and bacteria, respectively. Meanwhile, invertebrate richness remained spatially unchanged but varied across seasons. The structure of local food webs, such as link density and nestedness, also varied across space and time. However, these patterns did not necessarily mirror those observed for biodiversity and functional feeding characteristics. Our results suggest that biodiversity patterns and food-web dynamics are not directly scalable to each other even at the same spatial and temporal scales. In order to conserve species diversity as well as the functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied.

By sampling environmental DNA across a large riverine network over multiple seasons, the varied dynamics between biodiversity and food-web dynamics are revealed.

Nested structure is dependent on visitor sex in the flower‒visitor networks in Kyoto, Japan

The characteristics of flower‒visitor networks, comprised of multiple species interacting with each other, predict ecological and evolutionary processes. Intraspecific and interspecific variations in interaction patterns should affect network structures. Because female and male visitors usually differ in flower-visiting patterns due to mating strategy, visitor sex should affect nestedness, in which specialist species interact with a subset of species that interact with generalist species. I hypothesized that a network of male visitors and flowering plants would be more nested than a female network because males are less picky about which flowers they visit. To examine the effect of visitor sex on nestedness, I used museum specimens of insects and built 11 flower-visitor species networks, each composed of female and male subnetworks, and compared the strength of nestedness and related network metrics between the subnetworks. I found that male subnetworks were significantly more nested than female ones, and species networks were less nested than male or female subnetworks. The result may be attributable to the by-chance selection of flowers by males. Because a nested structure is predicted to promote community stability in mutualistic flower-visitor networks, the greater nestedness of male subnetworks may suggest a positive effect of male visitors on pollination community stability.

Changes in plant-herbivore network structure and robustness along land-use intensity gradients in grasslands and forests

Land-use intensification poses major threats to biodiversity, such as to insect herbivore communities. The stability of these communities depends on interactions linking herbivores and host plants. How interaction network structure begets robustness, and thus stability, in different ecosystems and how network structure and robustness are altered along land-use intensity gradients are unclear. We analyzed plant-herbivore networks based on literature-derived interactions and long-term sampling from 289 grasslands and forests in three regions of Germany. Network size and nestedness were the most important determinants of network robustness in both ecosystems. Along land-use intensity gradients, networks in moderately grazed grasslands were more robust than in those managed by frequent mowing or fertilization. In forests, changes of network robustness along land-use intensity gradients relied on changes in plant species richness. Our results expand our knowledge of the stability of plant-herbivore networks and indicate options for management aimed at stabilizing herbivore communities.

An ecological approach to structural flexibility in online communication systems

Human cognitive abilities are limited resources. Today, in the age of cheap information-cheap to produce, to manipulate, to disseminate-this cognitive bottleneck translates into hypercompetition for rewarding outcomes among actors. These incentives push actors to mutualistically interact with specific memes, seeking the virality of their messages. In turn, memes' chances to persist and spread are subject to changes in the communication environment. In spite of all this complexity, here we show that the underlying architecture of empirical actor-meme information ecosystems evolves into recurring emergent patterns. We then propose an ecology-inspired modelling framework, bringing to light the precise mechanisms causing the observed flexible structural reorganisation. The model predicts-and the data confirm-that users' struggle for visibility induces a re-equilibration of the network's mesoscale towards self-similar nested arrangements. Our final microscale insights suggest that flexibility at the structural level is not mirrored at the dynamical one.

Behaviour moderates the impacts of food-web structure on species coexistence

How species coexistence (mathematical 'feasibility') in food webs emerges from species' trophic interactions remains a long-standing open question. Here we investigate how structure (network topology and body-size structure) and behaviour (foraging strategy and spatial dimensionality of interactions) interactively affect feasibility in food webs. Metabolically-constrained modelling of food-web dynamics based on whole-organism consumption revealed that feasibility is promoted in systems dominated by large-eat-small foraging (consumers eating smaller resources) whenever (1) many top consumers are present, (2) grazing or sit-and-wait foraging strategies are common, and (3) species engage in two-dimensional interactions. Congruently, the first two conditions were associated with dominance of large-eat-small foraging in 74 well-resolved (primarily aquatic) real-world food webs. Our findings provide a new, mechanistic understanding of how behavioural properties can modulate the effects of structural properties on species coexistence in food webs, and suggest that 'being feasible' constrains the spectra of behavioural and structural properties seen in natural food webs.

Measuring nestedness: A comparative study of the performance of different metrics

Nestedness is a property of interaction networks widely observed in natural mutualistic communities, among other systems. A perfectly nested network is characterized by the peculiarity that the interactions of any node form a subset of the interactions of all nodes with higher degree. Despite a widespread interest on this pattern, no general consensus exists on how to measure it. Instead, several nestedness metrics, based on different but not necessarily independent properties of the networks, coexist in the literature, blurring the comparison between ecosystems. In this work, we present a detailed critical study of the behavior of six nestedness metrics and the variants of two of them. In order to evaluate their performance, we compare the obtained values of the nestedness of a large set of real networks among them and against a maximum-entropy and maximum-likelihood null model. We also analyze the dependencies of each metrics on different network parameters, as size, fill, and eccentricity. Our results point out, first, that the metrics do not rank networks universally in terms of their degree of nestedness. Furthermore, several metrics show significant dependencies on the network properties considered. The study of these dependencies allows us to understand some of the observed systematic shifts against the null model. Altogether, this paper intends to provide readers with a critical guide on how to measure nestedness patterns, by explaining the functioning of several metrics and disclosing their qualities and flaws. Besides, we also aim to extend the application of null models based on maximum entropy to the scarcely explored area of ecological networks. Finally, we provide a fully documented repository that allows constructing the null model and calculating the studied nestedness indexes. In addition, it provides the probability matrices to build the null model for a large dataset of more than 200 bipartite networks.

Asymmetric interactions of seed-predation network contribute to rare-species advantage

Although the asymmetry of species linkage within ecological networks is now well recognized, its effect on communities has scarcely been empirically investigated. Based on theory, we predicted that an asymmetric architecture of antagonistic plant-herbivore networks would emerge at the community level and that this asymmetry would negatively affect community-common plants more than rare ones. We tested this prediction by analyzing the architectural properties of an alpine plant and pre-dispersal seed-predator network and its effect on seed loss rate of plants in the Tibetan Plateau. This network showed an asymmetric architecture, where the common plant species (with a larger aboveground biomass per area) were infested by a higher number of predator species. Moreover, they asymmetrically interacted with specialized herbivores, presumably because of greater seed resource abundance. In turn, the asymmetric interactions led to a higher proportion of seed loss in the common plants at the species level. Our results suggest that asymmetric antagonistic networks may improve species coexistence by contributing to a mechanism of rare-species advantage.

Predation risk influences food-web structure by constraining species diet choice

The foraging behaviour of species determines their diet and, therefore, also emergent food-web structure. Optimal foraging theory (OFT) has previously been applied to understand the emergence of food-web structure through a consumer-centric consideration of diet choice. However, the resource-centric viewpoint, where species adjust their behaviour to reduce the risk of predation, has not been considered. We develop a mechanistic model that merges metabolic theory with OFT to incorporate the effect of predation risk on diet choice to assemble food webs. This 'predation-risk-compromise' (PR) model better captures the nestedness and modularity of empirical food webs relative to the classical optimal foraging model. Specifically, compared with optimal foraging alone, risk-mitigated foraging leads to more-nested but less-modular webs by broadening the diet of consumers at intermediate trophic levels. Thus, predation risk significantly affects food-web structure by constraining species' ability to forage optimally, and needs to be considered in future work.

Host specificity of parasitoids (Encyrtidae) toward armored scale insects (Diaspididae): Untangling the effect of cryptic species on quantitative food webs

Host specificity of parasitoids may be measured by various specialization indices to assess the variation of interaction strength among species and the structure of the wider interaction network. However, the conclusions from analyses at the species and network levels may differ, which remains poorly explored. In addition, the recovery of cryptic species of hosts and parasitoids with molecular data may affect the structure of inferred interaction links. We quantified host specificity of hymenopteran parasitoids (family Encyrtidae) on armored scale insects (Hemiptera: Diaspididae) from a wide geographic sampling range across the Chinese Mainland based on both morphological and molecular species delimitation. Mitochondrial COI and nuclear 28S markers detected high cryptic species diversity in the encyrtids and to a lesser degree in the diaspidids, which divided generalist morphospecies into complexes of specialists and generalists. One-to-one reciprocal host-parasite links were increased in the molecular data set, but different quantitative species-level indices produced contrasting estimates of specificity from various one-to-multiple and multiple-to-multiple host-parasite links. Network indices calculated from DNA-based species, compared to morphology-based species definitions, showed lower connectance and generality, but greater specialization and compartmentalization of the interaction network. We conclude that a high degree of cryptic species in host-parasitoid systems refines the true network structure and may cause us overestimating the stability of these interaction webs.

Bipartite graphs in systems biology and medicine: a survey of methods and applications

The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.

Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability

Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant-pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems.

Nestedness across biological scales

Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness throughout biological scales can stimulate the debate on how pervasive nestedness may be in nature, while the theoretical emergent principles can aid further research on commonalities of biological networks.

Biomass Reallocation between Juveniles and Adults Mediates Food Web Stability by Distributing Energy Away from Strong Interactions

Ecological theory has uncovered dynamical differences between food web modules (i.e. low species food web configurations) with only species-level links and food web modules that include within-species links (e.g. non-feeding links between mature and immature individuals) and has argued that these differences ought to cause food web theory that includes within-species links to contrast with classical food web theory. It is unclear, however, if life-history will affect the observed connection between interaction strength and stability in species-level theory. We show that when the predator in a species-level food chain is split into juvenile and adult stages using a simple nested approach, stage-structure can mute potentially strong interactions through the transfer of biomass within a species. Within-species biomass transfer distributes energy away from strong interactions promoting increased system stability consistent with classical food web theory.

Human Impacts and Climate Change Influence Nestedness and Modularity in Food-Web and Mutualistic Networks

Theoretical studies have indicated that nestedness and modularity—non-random structural patterns of ecological networks—influence the stability of ecosystems against perturbations; as such, climate change and human activity, as well as other sources of environmental perturbations, affect the nestedness and modularity of ecological networks. However, the effects of climate change and human activities on ecological networks are poorly understood. Here, we used a spatial analysis approach to examine the effects of climate change and human activities on the structural patterns of food webs and mutualistic networks, and found that ecological network structure is globally affected by climate change and human impacts, in addition to current climate. In pollination networks, for instance, nestedness increased and modularity decreased in response to increased human impacts. Modularity in seed-dispersal networks decreased with temperature change (i.e., warming), whereas food web nestedness increased and modularity declined in response to global warming. Although our findings are preliminary owing to data-analysis limitations, they enhance our understanding of the effects of environmental change on ecological communities.

Food-web complexity, meta-community complexity and community stability

What allows interacting, diverse species to coexist in nature has been a central question in ecology, ever since the theoretical prediction that a complex community should be inherently unstable. Although the role of spatiality in species coexistence has been recognized, its application to more complex systems has been less explored. Here, using a meta-community model of food web, we show that meta-community complexity, measured by the number of local food webs and their connectedness, elicits a self-regulating, negative-feedback mechanism and thus stabilizes food-web dynamics. Moreover, the presence of meta-community complexity can give rise to a positive food-web complexity-stability effect. Spatiality may play a more important role in stabilizing dynamics of complex, real food webs than expected from ecological theory based on the models of simpler food webs.

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity-invasion resistance relationships in bacterial rhizosphere communities.

Stability of competition-antagonism-mutualism hybrid community and the role of community network structure

Theory predicts that ecological communities of many interacting species are unstable, despite the fact that complex ecosystems persist in nature. A recent theoretical study hypothesised that coexistence of antagonism and mutualism can stabilise a community and even give rise to a positive complexity-stability relationship. Here, using a theoretical model, we extended the earlier hypothesis to include competition as a third major interaction type, and showed that interaction-type diversity generally enhances stability of complex communities. Furthermore, we report a new finding that the hierarchically structured antagonistic interaction network is important for the stabilizing effect of interaction type diversity to emerge in complex communities. The present study indicated that the complexities characterised by species number, connectance, species variation, and interaction type diversity synergistically contributed to maintaining communities, and posed an interesting question of how present complex communities emerged, and developed from simpler ecosystems.

Climatic seasonality may affect ecological network structure: food webs and mutualistic networks

Ecological networks exhibit non-random structural patterns, such as modularity and nestedness, which determine ecosystem stability with species diversity and connectance. Such structure-stability relationships are well known. However, another important perspective is less well understood: the relationship between the environment and structure. Inspired by theoretical studies that suggest that network structure can change due to environmental variability, we collected data on a number of empirical food webs and mutualistic networks and evaluated the effect of climatic seasonality on ecological network structure. As expected, we found that climatic seasonality affects ecological network structure. In particular, an increase in modularity due to climatic seasonality was observed in food webs; however, it is debatable whether this occurs in mutualistic networks. Interestingly, the type of climatic seasonality that affects network structure differs with ecosystem type. Rainfall and temperature seasonality influence freshwater food webs and mutualistic networks, respectively; food webs are smaller, and more modular, with increasing rainfall seasonality. Mutualistic networks exhibit a higher diversity (particularly of animals) with increasing temperature seasonality. These results confirm the theoretical prediction that the stability increases with greater perturbation. Although these results are still debatable because of several limitations in the data analysis, they may enhance our understanding of environment-structure relationships.

Empirical evaluation of neutral interactions in host-parasite networks

While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analyzed the concordance between neutral expectations and empirical observations at interaction, species, and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait matching would determine potential interactions between species, while abundance would determine their realization.

Coexistence of mutualists and non-mutualists in a dual-lattice model

Evolution and maintenance of mutualism have been one of the major questions in evolutionary ecology, because it is often susceptible of invasion of non-mutualistic strategy. Some previous studies using dual-lattice model suggest that spatial structures of habitat can prevent non-mutualism from prevailing over mutualism, while the detail of the dynamics is not fully revealed. Here we explore population dynamics of the two strategies (mutualism and non-mutualism) in two species engaged in Prisoner's Dilemma game on a dual-lattice space, especially focusing on whether mutualists and non-mutualists can coexist in long-term dynamics. The habitat consists of two layers, each of which a population of species inhabits, and interspecific interaction is restricted between two corresponding sites of the layers. Each individual of the both species is either a mutualist or a non-mutualist and only the former pay cost c for benefit of the partner b. The payoff of the game affects the individuals' fecundity, while the mortality is constant. Reproduction is restricted to neighboring vacant sites of the focal individuals. Our computer simulations of the model show that even if b/c ratio remains constant, mutualists become dominant in both species over wider ranges of basic reproduction rate (reproduction rate without interspecific interaction) as b and c increase. If basic reproduction rates are asymmetric between the species or basic reproduction rates were sufficiently large, mutualists and non-mutualists can coexist in one or both species, while their population sizes often fluctuate. Transition of the final state between mutualism and non-mutualism happens rather discontinuously, then total population sizes change drastically at the transition. Moreover, we also find paradoxical cases of unilateral exploitation, i.e. one species consists of mutualists and other species non-mutualists. Additional simulations reveal that accidental extinction of the non-mutualists of one species can result in extinction of mutualist of the other species.

Interaction intimacy organizes networks of antagonistic interactions in different ways

Interaction intimacy, the degree of biological integration between interacting individuals, shapes the ecology and evolution of species interactions. A major question in ecology is whether interaction intimacy also shapes the way interactions are organized within communities. We combined analyses of network structure and food web models to test the role of interaction intimacy in determining patterns of antagonistic interactions, such as host-parasite, predator-prey and plant-herbivore interactions. Networks describing interactions with low intimacy were more connected, more nested and less modular than high-intimacy networks. Moreover, the performance of the models differed across networks with different levels of intimacy. All models reproduced well low-intimacy networks, whereas the more elaborate models were also capable of reproducing networks depicting interactions with higher levels of intimacy. Our results indicate the key role of interaction intimacy in organizing antagonisms, suggesting that greater interaction intimacy might be associated with greater complexity in the assembly rules shaping ecological networks.

Emergence of structural patterns in neutral trophic networks

Interaction networks are central elements of ecological systems and have very complex structures. Historically, much effort has focused on niche-mediated processes to explain these structures, while an emerging consensus posits that both niche and neutral mechanisms simultaneously shape many features of ecological communities. However, the study of interaction networks still lacks a comprehensive neutral theory. Here we present a neutral model of predator-prey interactions and analyze the structural characteristics of the simulated networks. We find that connectance values (complexity) and complexity-diversity relationships of neutral networks are close to those observed in empirical bipartite networks. High nestedness and low modularity values observed in neutral networks fall in the range of those from empirical antagonist bipartite networks. Our results suggest that, as an alternative to niche-mediated processes that induce incompatibility between species ("niche forbidden links"), neutral processes create "neutral forbidden links" due to uneven species abundance distributions and the low probability of interaction between rare species. Neutral trophic networks must be seen as the missing endpoint of a continuum from niche to purely stochastic approaches of community organization.

Probabilistic patterns of interaction: the effects of link-strength variability on food web structure

Patterns of species interactions affect the dynamics of food webs. An important component of species interactions that is rarely considered with respect to food webs is the strengths of interactions, which may affect both structure and dynamics. In natural systems, these strengths are variable, and can be quantified as probability distributions. We examined how variation in strengths of interactions can be described hierarchically, and how this variation impacts the structure of species interactions in predator-prey networks, both of which are important components of ecological food webs. The stable isotope ratios of predator and prey species may be particularly useful for quantifying this variability, and we show how these data can be used to build probabilistic predator-prey networks. Moreover, the distribution of variation in strengths among interactions can be estimated from a limited number of observations. This distribution informs network structure, especially the key role of dietary specialization, which may be useful for predicting structural properties in systems that are difficult to observe. Finally, using three mammalian predator-prey networks (two African and one Canadian) quantified from stable isotope data, we show that exclusion of link-strength variability results in biased estimates of nestedness and modularity within food webs, whereas the inclusion of body size constraints only marginally increases the predictive accuracy of the isotope-based network. We find that modularity is the consequence of strong link-strengths in both African systems, while nestedness is not significantly present in any of the three predator-prey networks.

The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids

Characterizing the architecture of bipartite networks is increasingly used as a framework to study biotic interactions within their ecological context and to assess the extent to which evolutionary constraint shape them. Orchid mycorrhizal symbioses are particularly interesting as they are viewed as more beneficial for plants than for fungi, a situation expected to result in an asymmetry of biological constraint. This study addressed the architecture and phylogenetic constraint in these associations in tropical context. We identified a bipartite network including 73 orchid species and 95 taxonomic units of mycorrhizal fungi across the natural habitats of Reunion Island. Unlike some recent evidence for nestedness in mycorrhizal symbioses, we found a highly modular architecture that largely reflected an ecological barrier between epiphytic and terrestrial subnetworks. By testing for phylogenetic signal, the overall signal was stronger for both partners in the epiphytic subnetwork. Moreover, in the subnetwork of epiphytic angraecoid orchids, the signal in orchid phylogeny was stronger than the signal in fungal phylogeny. Epiphytic associations are therefore more conservative and may co-evolve more than terrestrial ones. We suggest that such tighter phylogenetic specialization may have been driven by stressful life conditions in the epiphytic niches. In addition to paralleling recent insights into mycorrhizal networks, this study furthermore provides support for epiphytism as a major factor affecting ecological assemblage and evolutionary constraint in tropical mycorrhizal symbioses.

Do food web models reproduce the structure of mutualistic networks?

Background

Simple models inspired by processes shaping consumer-resource interactions have helped to establish the primary processes underlying the organization of food webs, networks of trophic interactions among species. Because other ecological interactions such as mutualisms between plants and their pollinators and seed dispersers are inherently based in consumer-resource relationships we hypothesize that processes shaping food webs should organize mutualistic relationships as well.

Methodology/Principal Findings

We used a likelihood-based model selection approach to compare the performance of food web models and that of a model designed for mutualisms, in reproducing the structure of networks depicting mutualistic relationships. Our results show that these food web models are able to reproduce the structure of most of the mutualistic networks and even the simplest among the food web models, the cascade model, often reproduce overall structural properties of real mutualistic networks.

Conclusions/Significance

Based on our results we hypothesize that processes leading to feeding hierarchy, which is a characteristic shared by all food web models, might be a fundamental aspect in the assembly of mutualisms. These findings suggest that similar underlying ecological processes might be important in organizing different types of interactions.

The ecological and evolutionary implications of merging different types of networks

Interactions among species drive the ecological and evolutionary processes in ecological communities. These interactions are effectively key components of biodiversity. Studies that use a network approach to study the structure and dynamics of communities of interacting species have revealed many patterns and associated processes. Historically these studies were restricted to trophic interactions, although network approaches are now used to study a wide range of interactions, including for example the reproductive mutualisms. However, each interaction type remains studied largely in isolation from others. Merging the various interaction types within a single integrative framework is necessary if we want to further our understanding of the ecological and evolutionary dynamics of communities. Dividing the networks up is a methodological convenience as in the field the networks occur together in space and time and will be linked by shared species. Herein, we outline a conceptual framework for studying networks composed of more than one type of interaction, highlighting key questions and research areas that would benefit from their study.