Evaluation of ecological network analysis: Validation of output

Ecological network analysis (ENA) is a modeling approach increasingly being used to evaluate food webs and provide an ecosystem-based approach to resource management. Unfortunately, validation of ENA output is rarely performed. This study represents part of a larger effort to critically evaluate ENA. Here we validate ENA output using stable isotope analysis (SIA), and where validation is not met, determine the effects of modifying trophic networks to reflect validation.     

What is hidden behind the concept of ecosystem efficiency in energy transformation?

The number of energy transformation levels in trophic webs is usually below five, but can be extended up to ten when parasites and hyper-parasites are included. Research on the structure and function of food webs is relevant to the complexity–stability–productivity debate. The aim of this theoretical analysis is to link energetic and connectional aspects of ecosystems with information theory. Updating an energetic model reported by Ricklefs [Ecologia, Zanichelli Editore S.p.A., Bologna, Italy, 1993, p. 896], our approach is integrated with a static analysis of food webs. The length of food webs is theoretically associated with the average ecological efficiency which can be empirically correlated with the effective connectance between species. Furthermore, the advantage of greater complexity when applied to a signalling network is qualitatively addressed.The overall efficiency of energy transformation into biomass throughout a trophic web, in an ecosystem with a given number of species, is the resultant of the various ecological efficiencies, η, at the transitions between the trophic levels. However, we propose that an increment in effective connectance and interspecies connectivity based on a superimposed signalling web may increase the η values, despite the fact that signalling per se has an energetic cost. According to this hypothesis, ecosystem stability would not be necessarily reduced by increasing the number of trophic levels, N, whenever stability in terms of persistence is improved by a cost-efficient regulatory network.     

Network mutualism: Positive community-level relations in ecosystems

Empirically observable energy and matter transfers in ecosystems create network structures commonly called food webs. The relation or interaction type associated with each link between pair-wise objects can be classified as (+, −) or (−, +) depending on the net gain or loss experienced by each object. If objects are not adjacent in the food web, then their observed direct interaction is neutralism (0, 0). From this perspective, a zero-sum balance exists between the number of positive and negative relations in the ecosystem. However, community-level relations arise from observable direct and unobservable indirect pathways within a food web, giving rise to indirectly mediated relations, mutualism (+, +) and competition (−, −). Determination of community-level relations requires a systemic or holistic approach. Utility measures from environ analysis in the broader frame of ecological network analysis (ENA) provide such a methodology to investigate the relations resulting from all observed and indirect transfers. This research demonstrates the methodology and shows three important results from the analysis. First, all objects in ecological networks are related either through their input and output environs, and therefore all objects interact with and influence the others in the web: there are no null community-level relations. Second, the community-level relations can and do differ from direct relations: what you see is not always what you get. Third, due to the web of trophic and non-trophic interactions, community-level relations usually have a greater occurrence of mutualism than competition making them more positive than the direct relations that produced them: this is the property called network mutualism.     

Trophic levels and trophic tangles: the prevalence of omnivory in real food webs

The concept of trophic levels is one of the oldest in ecology and informs our understanding of energy flow and top-down control within food webs, but it has been criticized for ignoring omnivory. We tested whether trophic levels were apparent in 58 real food webs in four habitat types by examining patterns of trophic position. A large proportion of taxa (64.4%) occupied integer trophic positions, suggesting that discrete trophic levels do exist. Importantly however, the majority of those trophic positions were aggregated around integer values of 0 and 1, representing plants and herbivores. For the majority of the real food webs considered here, secondary consumers were no more likely to occupy an integer trophic position than in randomized food webs. This means that, above the herbivore trophic level, food webs are better characterized as a tangled web of omnivores. Omnivory was most common in marine systems, rarest in streams, and intermediate in lakes and terrestrial food webs. Trophic-level-based concepts such as trophic cascades may apply to systems with short food chains, but they become less valid as food chains lengthen.     

On the consequences of aggregation and balancing of networks on system properties derived from ecological network analysis

In the ecological network analysis (ENA) of complex flow food webs the assumption is often made that the models characterizing the flows and stocks of ecosystems occur in a steady state where inflows equals outflows. An assessment of the system indices derived from ENA of six balanced and unbalanced system models, respectively, indicate to differences between indices. The aggregation of highly articulated flow models into models with fewer compartments also has drastic effects on the system metrics, particularly on the information indices.     

Structuring pelagic trophic networks from the biomass size spectra

The selection and establishment of the structure (number and compartments, aggregation criteria, and trophic links) of the food webs is a critical task in trophic modelling. The present work proposes a systematic method to structure trophic networks in pelagic food webs. The biomass-size spectrum (BSS) is a well-established approach to analyze the structure of pelagic communities, and the body size is especially related to the ecological role of the organisms in the pelagic environment. To structure food webs, this work uses detailed arrangements of the community in size classes with increasing widths (like Sheldon-type BSS) as first aggregation criteria, and BSS theory as a framework to integrate the available knowledge about feeding selectivity in order to obtain a method to identify the trophic links between compartments. Diet composition matrices were estimated through the combination of a probability of encounter for each food type and a specific probability of ingestion related to the food size selectivity and other food quality characteristics (e.g., morphology and nutritional quality). The feasibility of this approach has been illustrated through data of size-structured communities extracted from the literature including different planktonic predator guilds (nanoflagellates, cladoceran-dominated zooplankton and copepod-dominated zooplankton) in a high mountain lake (La Caldera, Spain), two subtropical wetland lakes (meso-oligotrophic Laguna Galarza and eutrophic Laguna Iberá, Argentina) and a marine microcosm (Alborán Sea, Mediterranean). The identification of “who eats whom” and “by how much” also allows for more accurate analyses of the trophic control in the BSS. Extensive analyses of the balance between top-down and bottom-up controls were developed for the feeding interactions of the study cases.     

Invasive species impacts on ecosystem structure and function: A comparison of Oneida Lake, New York, USA, before and after zebra mussel invasion

Exotic species invasion is widely considered to affect ecosystem structure and function. Yet, few contemporary approaches can assess the effects of exotic species invasion at such an inclusive level. Our research presents one of the first attempts to examine the effects of an exotic species at the ecosystem level in a quantifiable manner. We used ecological network analysis (ENA) and a social network analysis (SNA) method called cohesion analysis to examine the effect of zebra mussel (Dreissena polymorpha) invasion on the Oneida Lake, New York, USA, food web. We used ENA to quantify ecosystem function through an analysis of food web carbon transfer that explicitly incorporated flow over all food web paths (direct and indirect). The cohesion analysis assessed ecosystem structure through an organization of food web members into subgroups of strongly interacting predators and prey. Our analysis detected effects of zebra mussel invasion throughout the entire Oneida Lake food web, including changes in trophic flow efficiency (i.e., carbon flow among trophic levels) and alterations of food web organization (i.e., paths of carbon flow) and ecosystem activity (i.e., total carbon flow). ENA indicated that zebra mussels altered food web function by shunting carbon from pelagic to benthic pathways, increasing dissipative flow loss, and decreasing ecosystem activity. SNA revealed the strength of zebra mussel perturbation as evidenced by a reorganization of food web subgroup structure, with a decrease in importance of pelagic pathways, a concomitant rise of benthic pathways, and a reorganization of interactions between top predator fish. Together, these analyses allowed for a holistic understanding of the effects of zebra mussel invasion on the Oneida Lake food web.     

Adaptations in a hierarchical food web of southeastern Lake Michigan

Two issues in ecological network theory are: (1) how to construct an ecological network model and (2) how do entire networks (as opposed to individual species) adapt to changing conditions? We present a novel method for constructing an ecological network model for the food web of southeastern Lake Michigan (USA) and we identify changes in key system properties that are large relative to their uncertainty as this ecological network adapts from one time point to a second time point in response to multiple perturbations. To construct our food web for southeastern Lake Michigan, we followed the list of seven recommendations outlined in Cohen et al. [Cohen, J.E., et al., 1993. Improving food webs. Ecology 74, 252–258] for improving food webs. We explored two inter-related extensions of hierarchical system theory with our food web; the first one was that subsystems react to perturbations independently in the short-term and the second one was that a system's properties change at a slower rate than its subsystems’ properties. We used Shannon's equations to provide quantitative versions of the basic food web properties: number of prey, number of predators, number of feeding links, and connectance (or density). We then compared these properties between the two time-periods by developing distributions of each property for each time period that took uncertainty about the property into account. We compared these distributions, and concluded that non-overlapping distributions indicated changes in these properties that were large relative to their uncertainty. Two subsystems were identified within our food web system structure (p < 0.001). One subsystem had more non-overlapping distributions in food web properties between Time 1 and Time 2 than the other subsystem. The overall system had all overlapping distributions in food web properties between Time 1 and Time 2. These results supported both extensions of hierarchical systems theory. Interestingly, the subsystem with more non-overlapping distributions in food web properties was the subsystem that contained primarily benthic taxa, contrary to expectations that the identified major perturbations (lower phosphorous inputs and invasive species) would more greatly affect the subsystem containing primarily pelagic taxa. Future food-web research should employ rigorous statistical analysis and incorporate uncertainty in food web properties for a better understanding of how ecological networks adapt.     

Invasive species impacts on ecosystem structure and function: A comparison of the Bay of Quinte, Canada, and Oneida Lake, USA, before and after zebra mussel invasion

As invasion rates of exotic species increase, an ecosystem level understanding of their impacts is imperative for predicting future spread and consequences. We have previously shown that network analyses are powerful tools for understanding the effects of exotic species perturbation on ecosystems. We now use the network analysis approach to compare how the same perturbation affects another ecosystem of similar trophic status. We compared food web characteristics of the Bay of Quinte, Lake Ontario (Canada), to previous research on Oneida Lake, New York (USA) before and after zebra mussel (Dreissena polymorpha) invasion. We used ecological network analysis (ENA) to rigorously quantify ecosystem function through an analysis of direct and indirect food web transfers. We used a social network analysis method, cohesion analysis (CA), to assess ecosystem structure by organizing food web members into subgroups of strongly interacting predators and prey. Together, ENA and CA allowed us to understand how food web structure and function respond simultaneously to perturbation. In general, zebra mussel effects on the Bay of Quinte, when compared to Oneida Lake, were similar in direction, but greater in magnitude. Both systems underwent functional changes involving focused flow through a small number of taxa and increased use of benthic sources of production; additionally, both systems structurally changed with subgroup membership changing considerably (33% in Oneida Lake) or being disrupted entirely (in the Bay of Quinte). However, the response of total ecosystem activity (as measured by carbon flow) differed between both systems, with increasing activity in the Bay of Quinte, and decreasing activity in Oneida Lake. Thus, these analyses revealed parallel effects of zebra mussel invasion in ecosystems of similar trophic status, yet they also suggested that important differences may exist. As exotic species continue to disrupt the structure and function of our native ecosystems, food web network analyses will be useful for understanding their far-reaching effects.     

Linking trophic positions and flow structure constraints in ecological networks: Energy transfer efficiency or topology effect?

In the present work we investigate whether the distribution of energy flows in ecosystems responds to criteria of trophic organization. We analyzed weighted and unweighted food webs estimating, for each node, trophic position (TP), Shannon's index of inflow diversity (H) and individual contribution to the whole average mutual information (AMI). Finally, we performed the same analysis on simulated webs that were constructed using the following criteria: (a) preserving topology and varying link strength; (b) modifying position of links and their intensities.     

A simple random path method for the analysis of flow networks

The path of a particle through an ecosystem is modelled as a Markov chain. For a given flow network, powers of the transition matrix are used to calculate the distribution of the particles over the network after each transition. The method may be applied for the definition and calculation of trophic levels in food webs. The algorithm yields the trophic level distribution of species, the species composition of trophic levels, and the path length distribution of output flows. In addition, the network can be described as a linear chain, with the throughflows at each step identified. Data from several ecosystems are analyzed by the method, showing that surprising insights may result.     

Identifying key species in ecosystems with stochastic sensitivity analysis

The development of approaches to estimate the vulnerability of biological communities and ecosystems to extirpations and reductions of species is a central challenge of conservation biology. One key aim of this challenge is to develop quantitative approaches to estimate and rank interaction strengths and keystoneness of species and functional groups, i.e. to quantify the relative importance of species. Network analysis can be a powerful tool for this because certain structural aspects of ecological networks are good indicators of the mechanisms that maintain co-evolved, biotic interactions. A static view of ecological networks would lead us to focus research on highly-central species in food webs (topological key players in ecosystems). There are a variety of centrality indices, developed for several types of ecological networks (e.g. for weighted and un-weighted webs). However, truly understanding extinction and its community-wide effects requires the use of dynamic models. Deterministic dynamic models are feasible when population sizes are sufficiently large to minimize noise in the overall system. In models with small population sizes, stochasticity can be modelled explicitly. We present a stochastic simulation-based ecosystem model for identification of “dynamic key species” in situations where stochastic models are appropriate. To demonstrate this approach, we simulated ecosystem dynamics and performed sensitivity analysis using data from the Prince William Sound, Alaska ecosystem model. We then compare these results to those of purely topological analyses and deterministic dynamic (Ecosim) studies. We present the relationships between various topological and dynamic indices and discuss their biological relevance. The trophic group with the largest effect on others is nearshore demersals, the species mostly sensitive to others is halibut, and the group of both considerable effect on and sensitivity to others is juvenile herring. The most important trophic groups in our dynamical simulations appear to have intermediate trophic levels.     

Maximal yields from multispecies fisheries systems: rules for systems with multiple trophic levels.

Increasing centralization of the control of fisheries combined with increased knowledge of food-web relationships is likely to lead to attempts to maximize economic yield from entire food webs. With the exception of predator-prey systems, we lack any analysis of the nature of such yield-maximizing strategies. We use simple food-web models to investigate the nature of yield- or profit-maximizing exploitation of communities including two types of three-species food webs and a variety of six-species systems with as many as five trophic levels. These models show that, for most webs, relatively few species are harvested at equilibrium and that a significant fraction of the species is lost from the web. These extinctions occur for two reasons: (1) indirect effects due to harvesting of species that had positive effects on the extinct species, and (2) intentional eradication of species that are not themselves valuable, but have negative effects on more valuable species. In most cases, the yield-maximizing harvest involves taking only species from one trophic level. In no case was an unharvested top predator part of the yield-maximizing strategy. Analyses reveal that the existence of direct density dependence in consumers has a large effect on the nature of the optimal harvest policy, typically resulting in harvest of a larger number of species. A constraint that all species must be retained in the system (a "constraint of biodiversity conservation") usually increases the number of species and trophic levels harvested at the yield-maximizing policy. The reduction in total yield caused by such a constraint is modest for most food webs but can be over 90% in some cases. Independent harvesting of species within the web can also cause extinctions but is less likely to do so.     

Potential trophic biomasses and trace-substance concentrations in unstructured marine food webs

It is proposed that unstructured food webs may more closely resemble real marine food webs than does the conventional, structured model. An unstructured food-web model leads to a set of very simple expressions for the potential partition of matter in the food web in steady state, including the potential fluxes of material and biomasses of trophic types and the concentration of trace substances in the members and materials of such a food web. The approach may explain some anomalies of relative predator-prey biomasses and of trace-element distribution, and may be of further use for analyzing and predicting (a) the tropho-dynamic parameters of marine systems, (b) the trophic positions, and the steadystate fluxes and biomasses of marine organisms, (c) the distribution of trace materials in marine biota; and for relating findings among these areas. Other matters, such as limitations of food conversion, indicated by concentration factors of trace substances, the possibilities of non-causal association of anomalously high levels of trace substances (including pollutants) with diseased or otherwise abnormal marine creatures, and an inverse relationship of early concentrations of newly introduced trace substances and their eventual concentrations in various organisms, are also developed in this approach.     

Can stable isotope ratios provide for community-wide measures of trophic structure?

Stable isotope ratios (typically of carbon and nitrogen) provide one representation of an organism's trophic niche and are widely used to examine aspects of food web structure. Yet stable isotopes have not been applied to quantitatively characterize community-wide aspects of trophic structure (i.e., at the level of an entire food web). We propose quantitative metrics that can be used to this end, drawing on similar approaches from ecomorphology research. For example, the convex hull area occupied by species in delta13C-delta15N niche space is a representation of the total extent of trophic diversity within a food web, whereas mean nearest neighbor distance among all species pairs is a measure of species packing within trophic niche space. To facilitate discussion of opportunities and limitations of the metrics, we provide empirical and conceptual examples drawn from Bahamian tidal creek food webs. These examples illustrate how this methodology can be used to quantify trophic diversity and trophic redundancy in food webs, as well as to link individual species to characteristics of the food web in which they are embedded. Building from extensive applications of stable isotope ratios by ecologists, the community-wide metrics may provide a new perspective on food web structure, function, and dynamics.     

Indirect effects of an exploited predator on recruitment of coral-reef fishes

The more ecologists examine the role of trait-mediated indirect interactions (TMIIs), especially in regulating predator-prey interactions, the more we recognize their fundamental role in structuring food webs. However, most empirical evidence for TMIIs comes from studies that are either conducted in laboratory or mesocosm venues or are restricted to simple food webs involving lower trophic-level animals. Here, I quantified the direct and indirect effects of interactions between high-level vertebrate predators on their vertebrate prey using a field experiment. Specifically, I tested how varying densities of a large-bodied, top predator (Nassau grouper; Epinephelus striatus) affected persistence, growth, and behavior of two smaller-bodied, intermediate predators (coney and graysby groupers; Cephalopholis fulva and C. cruentata) on 20 isolated patch reefs in the Bahamas. Large-bodied groupers are capable of consuming their smaller-bodied counterparts, and previous observational studies have indicated that local abundances of these groupers are negatively correlated. I measured the effects of interactions among groupers on lower trophic-level prey by quantifying recruitment of coral-reef fishes to the reefs. The field experiment demonstrated a strong trophic cascade that was entirely mediated by modified behavior of the intermediate predators. These results indicate that indirect, nonlethal interactions in natural systems can have strong cascading effects even at high trophic levels and in high-diversity food webs. Incorporating the complexity of such indirect effects into fisheries management may improve the sustainability of fished populations and strengthen marine conservation efforts; however these results also indicate that the effects of fishing are complex and difficult to predict.     

砷在海洋食物链中的生物放大潜力及发生机制探讨

砷是世界范围内危害最大的环境污染物之一,也是近海区域一种常见污染物。本文综述了近年来砷在海洋生态系统中累积、转化及传递的最新研究进展。海洋生物普遍具有较高含量的砷,这些砷主要为低毒性的有机砷形态。砷在许多海洋食物链/网中被生物放大,造成高营养级生物中的砷富集,可对生物与人类健康产生潜在危害;这与砷在淡水食物链/网中普遍被生物减小的现象形成鲜明对比。海洋鱼类和贝类等生物可将吸收的无机砷通过生物转化合成砷甜菜碱等有机砷形态,而有机砷比无机砷具有更高的食物链传递能力,可导致海洋鱼类富集更高浓度的砷。因此,砷在海洋生物中的有机形态可能有助于砷沿着海洋食物链/网富集,在某些情况下被生物放大。今后应该加强对不同砷形态在海洋食物链/网中传递及相应影响因素的研究,并通过室内模拟实验与野外调查相结合进行验证,从而加深对砷的生态毒理和生物地球化学作用的科学认识,对准确评估预测砷的生态风险和保障海洋生态安全有重要意义。     

Ecological network analysis for water use systems—A case study of the Yellow River Basin

Ecological network analysis (ENA) is introduced in this paper as a promising approach to study water use systems. Information indices from ENA involving total system throughput (TST), ascendency and overhead are calculated here. Two related aspects including organization inherent in system structures and synthesized water use intensity related with sustainable development of water use systems are analyzed. The indices of ascendency and overhead are applied for analyzing and characterizing water use network organization. For comparison of sustainability of water use systems from integrated aspects of environment, society and economy and based on TST, a new indicator termed as total system throughput intensity (TSTI) is constructed incorporating parameters of land, precipitation, population, GDP and environmental flow, which can be used as a measure of sustainability in terms of synthesized water use intensity. The Yellow River Basin in China during 1998–2006 is chosen as the case study and divided into subsystems according to the six river sections as from source to Lanzhou (S1-L1), Lanzhou to Toudaoguai (L1-T), Toudaoguai to Longmen (T-L2), Longmen to Sanmenxia (L2-S2), Sanmenxia to Huayuankou (S2-H) and Huayuankou to the mouth of Bo Sea (H-B). The results show that (i) the organization levels of L1-T and H-B are better than those of S1-L1 and T-L2, with those of L2-S2 and S2-H the worst; (ii) the synthesized water use intensity has been improving, of which T-L2, L2-S2 and S2-H are at the highest levels while H-B the lowest. In addition, the comparison between TSTI and other metrics and the relationship between ascendency and TSTI are discussed, from which the importance of TSTI is reflected and the optimization criterions for sustainable development of six subsystems are derived. It can be concluded that the application of ENA in water use systems can provide new angles for water resource management to address the challenges of assessing and optimizing options to obtain more sustainable water use.