Examining the potential effects of species aggregation on the network structure of food webs

One of the key measures that have been used to describe the topological properties of complex networks is the “degree distribution”, which is a measure that describes the frequency distribution of number of links per node. Food webs are complex ecological networks that describe the trophic relationships among species in a community, and the topological properties of empirical food webs, including degree distributions, have been examined previously. Previously, the “niche model” has been shown to accurately predict degree distributions of empirical food webs, however, the niche model-generated food webs were referenced against empirical food webs that had their species grouped together based on their taxonomic and/or trophic relationships (aggregated food webs). Here, we explore the effects of species aggregation on the ability of the niche model to predict the total- (sum of prey and predator links per node), in- (number of predator links per node), and out- (number of prey links per node) degree distributions of empirical food webs by examining two food webs that can be aggregated at different levels of resolution. The results showed that (1) the cumulative total- and out-degree distributions were consistent with the niche model predictions when the species were aggregated, (2) when the species were disaggregated (i.e., higher resolution), there were mixed conclusions with regards to the niche model's ability to predict total- and out-degree distributions, (3) the model's ability to predict the in-degree distributions of the two food webs was generally inadequate. Although it has been argued that universal functional form based on the niche model could describe the degree distribution patterns of empirical food webs, we believe there are some limitations to the model's ability to accurately predict the structural properties of food webs.     

Emergence of non-random structure in local food webs generated from randomly structured regional webs

Previous studies have shown that high-resolution, empirical food webs possess a non-random network structure, typically characterized by uniform or exponential degree distributions. However, the empirical food webs that have been investigated for their structural properties represent local communities that are only a subset of a larger pool of regionally coexisting species. Here, we use a simple model to investigate the effects of regional food web structure on local food webs that are assembled by two simple processes: random immigration of species from a source web (regional food web), and random extinction of species within the local web. The model shows that local webs with non-random degree distributions can arise from randomly structured source webs. A comparison of local webs assembled from randomly structured source webs with local webs assembled from source webs generated by the niche model shows that the former have higher species richness at equilibrium, but have a nonlinear response to changing extinction rates. These results imply that the network structure of regional food webs can play a significant role in the assembly and dynamics of local webs in natural ecosystems. With natural landscapes becoming increasingly fragmented, understanding such structure may be a necessary key to understanding the maintenance and stability of local species diversity.     

Benthos as the basis for arctic lake food webs

Plankton have traditionally been viewed as the basis for limnetic food webs, with zooplankton acting as a gateway for energy passing between phytoplanktonic primary producers and fish. Often, benthic production has been considered to be important primarily in shallow systems or as a subsidy to planktonic food web pathways. Stable isotope food web analyses of two arctic lakes (NE14 and I minus) in the Toolik Lake region of Alaska indicate that benthos are the primary source of carbon for adults of all species of benthic and pelagic fish present. We found no effect of turbidity, which may suppress benthic algae by shading, on food web structure. Even though Secchi transparency varied from 10.2 m in NE14 to 0.55–2.6 m in I minus, food webs in both lakes were based upon benthos, had four trophic levels, and culminated with omnivorous lake trout. We suggest that the importance of benthos in the food webs of these lakes is due to their extreme oligotrophy, resulting in planktonic resources that are insufficient for the support of planktivorous consumers.     

Omnivory and the stability of food webs

The ecological concept of omnivory, feeding at more than a single trophic level, is formulated as an intermediate stage between any two of three classical three-dimensional species interaction systems-tritrophic chain, competition, and polyphagy. It is shown that omnivory may be either stabilizing or destabilizing, depending, in part, on the conditions of the parent systems from which it derives. It is further conjectured that the tritrophic to competition gradient cannot be entirely stable, that there must be an instability at some level of intermediate omnivory.     

Food webs: experts consuming families of experts

Food webs of habitats as diverse as lakes or desert valleys are known to exhibit common "food-web patterns", but the detailed mechanisms generating these structures have remained unclear. By employing a stochastic, dynamical model, we show that many aspects of the structure of predatory food webs can be understood as the traces of an evolutionary history where newly evolving species avoid direct competition with their relatives. The tendency to avoid sharing natural enemies (apparent competition) with related species is considerably weaker. Thus, "experts consuming families of experts" can be identified as the main underlying food-web pattern. We report the results of a systematic, quantitative model validation showing that the model is surprisingly accurate.     

Evidence for the existence of a robust pattern of prey selection in food webs

Food webs aim to provide a thorough representation of the trophic interactions found in an ecosystem. The complexity of empirical food webs, however, is leading many ecologists to focus dynamic ecosystem studies on smaller microcosm or mesocosm studies based upon community modules, which comprise three to five species and the interactions likely to have ecological relevance. We provide here a structural counterpart to community modules. We investigate food-web 'motifs' which are n-species connected subgraphs found within the food web. Remarkably, we find that the over- and under-representation of three-species motifs in empirical food webs can be understood through comparison to a static food-web model, the niche model. Our result conclusively demonstrates that predation upon species with some 'characteristic' niche value is the prey selection mechanism consistent with the structural properties of empirical food webs.     

Functional links and robustness in food webs

The robustness of ecosystems to species losses is a central question in ecology, given the current pace of extinctions and the many species threatened by human impacts, including habitat destruction and climate change. Robustness from the perspective of secondary extinctions has been addressed in the context of food webs to consider the complex network of species interactions that underlie responses to perturbations. In-silico removal experiments have examined the structural properties of food webs that enhance or hamper the robustness of ecosystems to species losses, with a focus on the role of hubs, the most connected species. Here we take a different approach and focus on the role of the connections themselves. We show that trophic links can be divided into functional and redundant based on their contribution to robustness. The analysis of empirical webs shows that hubs are not necessarily the most important species as they may hold many redundant links. Furthermore, the fraction of functional connections is high and constant across systems regardless of size and interconnectedness. The main consequence of this scaling pattern is that ecosystem robustness can be considerably reduced by species extinctions even when these do not result in any secondary extinctions. This introduces the possibility of tipping points in the collapse of ecosystems.     

Biodiversity maintenance in food webs with regulatory environmental feedbacks

Although the food web is one of the most fundamental and oldest concepts in ecology, elucidating the strategies and structures by which natural communities of species persist remains a challenge to empirical and theoretical ecologists. We show that simple regulatory feedbacks between autotrophs and their environment when embedded within complex and realistic food-web models enhance biodiversity. The food webs are generated through the niche-model algorithm and coupled with predator-prey dynamics, with and without environmental feedbacks at the autotroph level. With high probability and especially at lower, more realistic connectance levels, regulatory environmental feedbacks result in fewer species extinctions, that is, in increased species persistence. These same feedback couplings, however, also sensitize food webs to environmental stresses leading to abrupt collapses in biodiversity with increased forcing. Feedback interactions between species and their material environments anchor food-web persistence, adding another dimension to biodiversity conservation. We suggest that the regulatory features of two natural systems, deep-sea tubeworms with their microbial consortia and a soil ecosystem manifesting adaptive homeostatic changes, can be embedded within niche-model food-web dynamics.     

Quantitative food webs of dipteran leafminers and their parasitoids in Argentina

The quantitative structure of two host–parasitoid communities based on leaf-mining flies (Diptera, Agromyzidae) in Argentina is described. The two communities consisted of 29 and 27 hosts, 46 and 40 parasitoids, and 193 and 179 recorded host–parasitoid associations. Also, food webs were constructed for one community based solely on samples taken in the wet and dry seasons. Data were expressed as quantitative food webs, and the manner in which food web properties, such as connectance and compartmentalization, were influenced by sampling intensity was explored. The potential importance of indirect effects between hosts mediated by parasitoids (e.g. apparent competition) was assessed using quantitative parasitoid overlap diagrams. The studys results suggest that indirect effects are likely to be important in these highly connected communities. The limitations of the studys analysis, and how the conclusions can be tested experimentally, are discussed.     

Adaptive omnivory and species coexistence in tri-trophic food webs

The commonness of omnivory in natural communities is puzzling, because simple dynamic models of tri-trophic systems with omnivory are prone to species extinction. In particular, the intermediate consumer is frequently excluded by the omnivore at high levels of enrichment. It has been suggested that adaptive foraging by the omnivore may facilitate coexistence, because the intermediate consumer should persist more easily if it is occasionally dropped from the omnivore's diet. We explore theoretically how species permanence in tri-trophic systems is affected if the omnivore forages adaptively according to the "diet rule", i.e., feeds on the less profitable of its two prey species only if the more profitable one is sufficiently rare. We show that, compared to systems where omnivory is fixed, adaptive omnivory may indeed facilitate 3-species persistence. Counter to intuition, however, facilitation of 3-species coexistence requires that the intermediate consumer is a more profitable prey than the basal resource. Consequently, adaptive omnivory does not facilitate persistence of the intermediate consumer but enlarges the persistence region of the omnivore towards parameter space where a fixed omnivore would be excluded by the intermediate consumer. Overall, the positive effect of adaptive omnivory on 3-species persistence is, however, small. Generally, whether omnivory is fixed or adaptive, 3-species permanence is most likely when profitability (=conversion efficiency into omnivores) is low for basal resources and high for intermediate consumers.     

Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction

Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect–plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models.     

The impact of climate change on the structure of Pleistocene food webs across the mammoth steppe

Species interactions form food webs, impacting community structure and, potentially, ecological dynamics. It is likely that global climatic perturbations that occur over long periods of time have a significant influence on species interaction patterns. Here, we integrate stable isotope analysis and network theory to reconstruct patterns of trophic interactions for six independent mammalian communities that inhabited mammoth steppe environments spanning western Europe to eastern Alaska (Beringia) during the Late Pleistocene. We use a Bayesian mixing model to quantify the contribution of prey to the diets of local predators, and assess how the structure of trophic interactions changed across space and the Last Glacial Maximum (LGM), a global climatic event that severely impacted mammoth steppe communities. We find that large felids had diets that were more constrained than those of co-occurring predators, and largely influenced by an increase in Rangifer abundance after the LGM. Moreover, the structural organization of Beringian and European communities strongly differed: compared with Europe, species interactions in Beringian communities before—and possibly after—the LGM were highly modular. We suggest that this difference in modularity may have been driven by the geographical insularity of Beringian communities.     

Serological tracers of meiofaunal food webs

Serological methods utilizing taxon-specific antibodies were used to identify trophic connections in a salt marsh of South Carolina (U. S. A.). The incorporation of meiofauna within the benthic invertebrate food web was detected with these methods when microscopial examinations of predator stomachs revealed nothing but amorphous material and detritus. Measurements of soluble prey proteins in both predator guts and surficial sediments provided data to quantify the trophic connections. Difficulties with data interpretation limit the utility of serological methods for quantifying predation in the field.     

Networks in ecology

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Recently, ecology has shown a strong interest in network theory. The question, as with any other emerging field, is to what extent we are making real progress in understanding ecological and evolutionary processes or just telling the same stories with fancy new words. I first present a biased overview of the development of network theory, focusing on its search for common patterns across seemingly different systems. I then proceed by discussing some applications of network theory in ecology, namely, species interactions, spatial ecology, epidemiology, and evolution in social groups . Finally, I suggest important contributions of the network approach such as identifying the consequences of heterogeneity for population and community dynamics, potential pitfalls, and future directions.     

The impact of nonlinear functional responses on the long-term evolution of food web structure

We investigate the long-term web structure emerging in evolutionary food web models when different types of functional responses are used. We find that large and complex webs with several trophic layers arise only if the population dynamics is such that it allows predators to focus on their best prey species. This can be achieved using modified Lotka-Volterra or Holling/Beddington functional responses with effective couplings that depend on the predator's efficiency at exploiting the prey, or a ratio-dependent functional response with adaptive foraging. In contrast, if standard Lotka-Volterra or Holling/Beddington functional responses are used, long-term evolution generates webs with almost all species being basal, and with additionally many links between these species. Interestingly, in all cases studied, a large proportion of weak links result naturally from the evolution of the food webs.     

Energetics of microbial food webs

The energetic demand of microorganisms in natural waters and the flux of energy between microorganisms and metazoans has been evaluated by empirical measurements in nature, in microcosms and mesocosms, and by simulation models. Microorganisms in temperate and tropical waters often use half or more of the energy fixed by photosynthesis. Most simulations and some experimental results suggest significant energy transfer to metazoans, but empirical evidence is mixed. Considerations of the range of growth yields of microorganisms and the number of trophic transfers among them indicate major energy losses within microbial food webs. Our ability to verify and quantify these processes is limited by the variability of assimilation efficiency and uncertainty about the structure of microbial food webs. However, even a two-step microbial chain is a major energy sink. As an energetic link to metazoans, the detritus food web is inefficient, and its significance may have been overstated. There is not enough bacterial biomass associated with detritus to support metazoan detritivores. Much detritus is digestible by metazoans directly. Thus, metazoans and bacteria may to a considerable degree compete for a common resource. Microorganisms, together with metazoans, are important to the stability of planktonic communities through their roles as rapid mineralizers of organic matter, releasing inorganic nutrients. The competition for organic matter and the resultant rapid mineralization help maintain stable populations of phytoplankton in the absence of advective nutrient supply. At temperatures near O °C, bacterial metabolism is suppressed more than is the rate of photosynthesis. As a result, the products of the spring phytoplankton bloom in high-temperate latitudes are not utilized rapidly by bacteria. At temperatures below 0°C microbial food webs are neither energy sinks or links: they are suppressed. Because the underlying mechanism of low-temperature inhibition is not known, we cannot yet generalize about this as a control of food web processes. Microorganisms may operate on several trophic levels simultaneously. Therefore, the realism of the trophic level concept and the reality of the use of ecological efficiency calculations in ecosystem models is questionable.     

Emergence of complexity in evolving niche-model food webs

We have analysed mechanisms that promote the emergence of complex structures in evolving model food webs. The niche model is used to determine predator-prey relationships. Complexity is measured by species richness as well as trophic level structure and link density. Adaptive dynamics that allow predators to concentrate on the prey species they are best adapted to lead to a strong increase in species number but have only a small effect on the number and relative occupancy of trophic levels. The density of active links also remains small but a high number of potential links allows the network to adjust to changes in the species composition (emergence and extinction of species). Incorporating effects of body size on individual metabolism leads to a more complex trophic level structure: both the maximum and the average trophic level increase. So does the density of active links. Taking body size effects into consideration does not have a measurable influence on species richness. If species are allowed to adjust their foraging behaviour, the complexity of the evolving networks can also be influenced by the size of the external resources. The larger the resources, the larger and more complex is the food web it can sustain. Body size effects and increasing resources do not change size and the simple structure of the evolving networks if adaptive foraging is prohibited. This leads to the conclusion that in the framework of the niche model adaptive foraging is a necessary but not sufficient condition for the emergence of complex networks. It is found that despite the stabilising effect of foraging adaptation the system displays elements of self-organised critical behaviour.     

Multispecies food webs with diffusion

Using Liapunov's direct method, in this paper, it has been shown that the general Lotka-Volterra food web is stable without and with diffusion under each case of homogeneous reservoir and flux boundary conditions. However, for a three species food web with Holling's functional response the above general result regarding stability is not necessarily true. In such a case, conditions and regions for non-linear stability, without and with diffusion, have been derived. It is shown that such an otherwise unstable system may become stable with diffusion at least in a subregion of the positive octant of the state space.     

Relevance of evolutionary history for food web structure

Explaining the structure of ecosystems is one of the great challenges of ecology. Simple models for food web structure aim at disentangling the complexity of ecological interaction networks and detect the main forces that are responsible for their shape. Trophic interactions are influenced by species traits, which in turn are largely determined by evolutionary history. Closely related species are more likely to share similar traits, such as body size, feeding mode and habitat preference than distant ones. Here, we present a theoretical framework for analysing whether evolutionary history--represented by taxonomic classification--provides valuable information on food web structure. In doing so, we measure which taxonomic ranks better explain species interactions. Our analysis is based on partitioning of the species into taxonomic units. For each partition, we compute the likelihood that a probabilistic model for food web structure reproduces the data using this information. We find that taxonomic partitions produce significantly higher likelihoods than expected at random. Marginal likelihoods (Bayes factors) are used to perform model selection among taxonomic ranks. We show that food webs are best explained by the coarser taxonomic ranks (kingdom to class). Our methods provide a way to explicitly include evolutionary history in models for food web structure.