Shifting levels of ecological network's analysis reveals different system properties.

Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue 'Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.

Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands.

The continuing loss of global biodiversity has raised questions about the risk that species extinctions pose for the functioning of natural ecosystems and the services that they provide for human wellbeing. There is consensus that, on single trophic levels, biodiversity sustains functions; however, to understand the full range of biodiversity effects, a holistic and multitrophic perspective is needed. Here, we apply methods from ecosystem ecology that quantify the structure and dynamics of the trophic network using ecosystem energetics to data from a large grassland biodiversity experiment. We show that higher plant diversity leads to more energy stored, greater energy flow and higher community-energy-use efficiency across the entire trophic network. These effects of biodiversity on energy dynamics were not restricted to only plants but were also expressed by other trophic groups and, to a similar degree, in aboveground and belowground parts of the ecosystem, even though plants are by far the dominating group in the system. The positive effects of biodiversity on one trophic level were not counteracted by the negative effects on adjacent levels. Trophic levels jointly increased the performance of the community, indicating ecosystem-wide multitrophic complementarity, which is potentially an important prerequisite for the provisioning of ecosystem services.

Weighting and indirect effects identify keystone species in food webs.

Species extinctions are accelerating globally, yet the mechanisms that maintain local biodiversity remain poorly understood. The extinction of species that feed on or are fed on by many others (i.e. 'hubs') has traditionally been thought to cause the greatest threat of further biodiversity loss. Very little attention has been paid to the strength of those feeding links (i.e. link weight) and the prevalence of indirect interactions. Here, we used a dynamical model based on empirical energy budget data to assess changes in ecosystem stability after simulating the loss of species according to various extinction scenarios. Link weight and/or indirect effects had stronger effects on food-web stability than the simple removal of 'hubs', demonstrating that both quantitative fluxes and species dissipating their effects across many links should be of great concern in biodiversity conservation, and the potential for 'hubs' to act as keystone species may have been exaggerated to date.

Genotypic variation in foundation species generates network structure that may drive community dynamics and evolution.

Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrowleaf cottonwood), in a long-term, common garden experiment using a bipartite "genotype-species" network perspective. We combine this empirical work with a simulation experiment designed to further investigate how variation among individual tree genotypes can impact network structure. Three findings emerged: (1) the empirical "genotype-species network" exhibited significant network structure with modularity being greater than the highly conservative null model; (2) as would be expected given a modular network structure, the empirical network displayed significant positive arthropod co-occurrence patterns; and (3) furthermore, the simulations of "genotype-species" networks displayed variation in network structure, with modularity in particular clearly increasing, as genotypic variation increased. These results support the conclusion that genetic variation in a single species contributes to the structure of ecological interaction networks, which could influence eco-ogical dynamics (e.g., assembly and stability) and evolution in a community context.

Spatial heterogeneity in soil microbes alters outcomes of plant competition.

Plant species vary greatly in their responsiveness to nutritional soil mutualists, such as mycorrhizal fungi and rhizobia, and this responsiveness is associated with a trade-off in allocation to root structures for resource uptake. As a result, the outcome of plant competition can change with the density of mutualists, with microbe-responsive plant species having high competitive ability when mutualists are abundant and non-responsive plants having high competitive ability with low densities of mutualists. When responsive plant species also allow mutualists to grow to greater densities, changes in mutualist density can generate a positive feedback, reinforcing an initial advantage to either plant type. We study a model of mutualist-mediated competition to understand outcomes of plant-plant interactions within a patchy environment. We find that a microbe-responsive plant can exclude a non-responsive plant from some initial conditions, but it must do so across the landscape including in the microbe-free areas where it is a poorer competitor. Otherwise, the non-responsive plant will persist in both mutualist-free and mutualist-rich regions. We apply our general findings to two different biological scenarios: invasion of a non-responsive plant into an established microbe-responsive native population, and successional replacement of non-responders by microbe-responsive species. We find that resistance to invasion is greatest when seed dispersal by the native plant is modest and dispersal by the invader is greater. Nonetheless, a native plant that relies on microbial mutualists for competitive dominance may be particularly vulnerable to invasion because any disturbance that temporarily reduces its density or that of the mutualist creates a window for a non-responsive invader to establish dominance. We further find that the positive feedbacks from associations with beneficial soil microbes create resistance to successional turnover. Our theoretical results constitute an important first step toward developing a general understanding of the interplay between mutualism and competition in patchy landscapes, and generate qualitative predictions that may be tested in future empirical studies.

Unique pattern of molt leads to low intraindividual variation in feather mercury concentrations in penguins.

The authors hypothesized that the catastrophic annual molt of penguins (Sphenisciformes) would lead to reduced intraindividual variation of mercury concentrations in body feathers. While mean mercury concentrations varied significantly among 8 penguin species, intraindividual variability did not differ among species and was 3 times lower than values observed in other seabirds. The findings of the present study suggest that a single body feather collected at random per individual can be adequate to estimate mercury exposure at the population level in penguins.

Environ centrality reveals the tendency of indirect effects to homogenize the functional importance of species in ecosystems.

Ecologists and conservation biologists need to identify the relative importance of species to make sound management decisions and effectively allocate scarce resources. We introduce a new method, termed environ centrality, to determine the relative importance of a species in an ecosystem network with respect to ecosystem energy-matter exchange. We demonstrate the uniqueness of environ centrality by comparing it to other common centrality metrics and then show its ecological significance. Specifically, we tested two hypotheses on a set of 50 empirically based ecosystem network models. The first concerned the distribution of centrality in the community. We hypothesized that the functional importance of species would tend to be concentrated into a few dominant species followed by a group of species with lower, more even importance as is often seen in dominance-diversity curves. Second, we tested the systems ecology hypothesis that indirect relationships homogenize the functional importance of species in ecosystems. Our results support both hypotheses and highlight the importance of detritus and nutrient recyclers such as fungi and bacteria in generating the energy-matter flow in ecosystems. Our homogenization results suggest that indirect effects are important in part because they tend to even the importance of species in ecosystems. A core contribution of this work is that it creates a formal, mathematical method to quantify the importance species play in generating ecosystem activity by integrating direct, indirect, and boundary effects in ecological systems.

Functional integration of ecological networks through pathway proliferation.

Large-scale structural patterns commonly occur in network models of complex systems including a skewed node degree distribution and small-world topology. These patterns suggest common organizational constraints and similar functional consequences. Here, we investigate a structural pattern termed pathway proliferation. Previous research enumerating pathways that link species determined that as pathway length increases, the number of pathways tends to increase without bound. We hypothesize that this pathway proliferation influences the flow of energy, matter, and information in ecosystems. In this paper, we clarify the pathway proliferation concept, introduce a measure of the node-node proliferation rate, describe factors influencing the rate, and characterize it in 17 large empirical food-webs. During this investigation, we uncovered a modular organization within these systems. Over half of the food-webs were composed of one or more subgroups that were strongly connected internally, but weakly connected to the rest of the system. Further, these modules had distinct proliferation rates. We conclude that pathway proliferation in ecological networks reveals subgroups of species that will be functionally integrated through cyclic indirect effects.