Talk and workshop given at 11th INTECOL Congress, London, 22nd August 2013.

Acidity is a major driving variable in the ecology of fresh waters, and we sought to quantify macroecological patterns in stream food webs across a wide pH gradient. We postulated that a few generalist herbivore-detritivores would dominate the invertebrate assemblage at low pH, with more specialists grazers at high pH. We also expected a switch towards algae in the diet of all primary consumers as the pH increased. For 20 stream food webs across the British Isles, spanning pH 5.0-8.4 (the acid sites being at least partially culturally acidified), we characterised basal resources and primary consumers, using both gut contents analysis and stable isotopes to study resource use by the latter. We found considerable species turnover across the pH gradient, with generalist herbivore-detritivores dominating the primary consumer assemblage at low pH and maintaining grazing. These were joined or replaced at higher pH by a suite of specialist grazers, while many taxa that persisted across the pH gradient broadened the range of algae consumed as acidity declined and increased their ingestion of biofilm, whose nutritional quality was higher than that of coarse detritus. There was thus an increased overall reliance on algae at higher pH, both by generalist herbivore-detritivores and due to the presence of specialist grazers, although detritus was important even in non-acidic streams. Both the ability of acid-tolerant, herbivore-detritivores to exploit both autochthonous and allochthonous food and the low nutritional value of basal resources might render chemically recovering systems resistant to invasion by the specialist grazers and help explain the sluggish ecological recovery of fresh waters whose water chemistry has ameliorated.

Summary There has been a lack of software available to ecologists for the management, visualisation and analysis of ecological community and food web data. Researchers have been forced to implement their own data formats and software, often from scratch, resulting in duplicated effort and bespoke solutions that are difficult to apply to future analyses and comparative studies. We introduce Cheddar – an R package that provides standard, transparent implementations of a wide range of food web and community‐level analyses and plots, focussing on ecological network data that are augmented with estimates of body mass and/or numerical abundance. The package allows analysis of individual communities, as well as collections of communities, allowing examination of changes in structure through time, across environmental gradients, or due to experimental manipulations. Several commonly analysed food web data sets are included and used in worked examples. This is the first time these important features have been combined in a single package that helps improve research efficiency and serves as a unified framework for future development.

An understanding of the consequences of long-term environmental change for higher levels of biological organisation is essential for both theoretical and applied ecology. Here, we present four decades of data from the well-characterised Broadstone Stream community, detailing biological responses to amelioration of acidification and the recent invasion of a top predator (brown trout, Salmo trutta L.) that was previously excluded by low pH. After several decades of reductions in acidifying emissions, species characteristic of less acid conditions have started to invade or recolonise Broadstone and other European freshwaters, but these signs of biological recovery are still patchy and have lagged behind chemical recovery. One possible explanation for slow recovery is ecological inertia arising from the internal dynamics of the food web, a hypothesis we investigate here using a combination of surveys, experiments and mathematical modelling. The invasion of this hitherto invertebrate-dominated system by a large, generalist vertebrate predator could be expected to alter the structure and stability of the food web. Long-term survey data revealed that the community has experienced waves of invasions or irruptions of progressively larger predators since the 1970s, as pH has risen. Intra-annual fluctuations in prey populations have become increasingly damped and the mean abundance of many species has declined, although none of the previously common taxa have been lost. This suggests that predation, rather than simple chemical tolerance, plays a key role in determining the trajectory of recovery, as the top-down effects of the generalist predators spread diffusely through the reticulate food web. Dynamical simulations indicate that the food web may have become less robust over time as pH has risen and larger predators have become dominant. These results suggest that, though none of the original suite of large invertebrate predators has been driven to local extinction, such an eventual outcome is feasible.

An understanding of the consequences of long-term environmental change for higher levels of biological organisation is essential for both theoretical and applied ecology. Here, we present four decades of data from the well-characterised Broadstone Stream community, detailing biological responses to amelioration of acidification and the recent invasion of a top predator (brown trout, Salmo trutta L.) that was previously excluded by low pH. After several decades of reductions in acidifying emissions, species characteristic of less acid conditions have started to invade or recolonise Broadstone and other European freshwaters, but these signs of biological recovery are still patchy and have lagged behind chemical recovery. One possible explanation for slow recovery is ecological inertia arising from the internal dynamics of the food web, a hypothesis we investigate here using a combination of surveys, experiments and mathematical modelling.The invasion of this hitherto invertebrate-dominated system by a large, generalist vertebrate predator could be expected to alter the structure and stability of the food web. Long-term survey data revealed that the community has experienced waves of invasions or irruptions of progressively larger predators since the 1970s, as pH has risen. Intra-annual fluctuations in prey populations have become increasingly damped and the mean abundance of many species has declined, although none of the previously common taxa have been lost. This suggests that predation, rather than simple chemical tolerance, plays a key role in determining the trajectory of recovery, as the top-down effects of the generalist predators spread diffusely through the reticulate food web. Dynamical simulations indicate that the food web may have become less robust over time as pH has risen and larger predators have become dominant. These results suggest that, though none of the original suite of large invertebrate predators has been driven to local extinction, such an eventual outcome is feasible.

Ecological networks are typically complex constructions of species and their interactions. During the last decade, the study of networks has moved from static to dynamic analyses, and has attained a deeper insight into their internal structure, heterogeneity, and temporal and spatial resolution. Here, we review, discuss and suggest research lines in the study of the spatio-temporal heterogeneity of networks and their hierarchical nature. We use case study data from two well-characterized model systems (the food web in Broadstone Stream in England and the pollination network at Zackenberg in Greenland), which are complemented with additional information from other studies. We focus upon eight topics: temporal dynamic space-for-time substitutions linkage constraints habitat borders network modularity individual-based networks invasions of networks and super networks that integrate different network types. Few studies have explicitly examined temporal change in networks, and we present examples that span from daily to decadal change: a common pattern that we see is a stable core surrounded by a group of dynamic, peripheral species, which, in pollinator networks enter the web via preferential linkage to the most generalist species. To some extent, temporal and spatial scales are interchangeable (i.e. networks exhibit ‘ergodicity’) and we explore how space-for-time substitutions can be used in the study of networks. Network structure is commonly constrained by phenological uncoupling (a temporal phenomenon), abundance, body size and population structure. Some potential links are never observed, that is they are ‘forbidden’ (fully constrained) or ‘missing’ (a sampling effect), and their absence can be just as ecologically significant as their presence. Spatial habitat borders can add heterogeneity to network structure, but their importance has rarely been studied: we explore how habitat generalization can be related to other resource dimensions. Many networks are hierarchically structured, with modules forming the basic building blocks, which can result in self-similarity. Scaling down from networks of species reveals another, finer-grained level of individual-based organization, the ecological consequences of which have yet to be fully explored. The few studies of individual-based ecological networks that are available suggest the potential for large intraspecific variance and, in the case of food webs, strong size-structuring. However, such data are still scarce and more studies are required to link individual-level and species-level networks. Invasions by alien species can be tracked by following the topological ‘career’ of the invader as it establishes itself within a network, with potentially important implications for conservation biology. Finally, by scaling up to a higher level of organization, it is possible to combine different network types (e.g. food webs and mutualistic networks) to form super networks, and this new approach has yet to be integrated into mainstream ecological research. We conclude by listing a set of research topics that we see as emerging candidates for ecological network studies in the near future.

Recent attempts to include more ecological detail in connectance food webs have revealed strong relationships between food web structure, species abundance and body size. Few studies, however, have assessed these and other macroecological patterns in food webs in order to examine how network structure, dynamics and their determinants change across environmental gradients. Here, we present 20 highly resolved, standardized stream food webs along a wide pH gradient (5.0-8.4). Our main goal of this study was to assess the influence of external environmental and internal biotic influences on community structure and stability. Many structural features of the food webs changed across the gradient, with web size, linkage density and complexity all increasing with pH. Chlorophyll-a concentrations in epilithic biofilms, as well as the biomass of macroinvertebrates and fish, were also positively correlated with pH. Directed connectance was not correlated with pH in our study, however, although some of the smallest food webs at the lowest pH displayed the highest connectance amongst the networks in this data set. The prevalence of generalism in such food webs, with many alternative food chains passing through any given species, might serve to confer a degree of stability upon these networks, if most feeding links are weak. We found clear differences between our allometrically inferred measures of per capita interaction strengths within the food web, with particularly strong links existing between herbivores and their algal resources and between fish and invertebrates, both of which also became more prevalent at high pH. Predatory interactions between invertebrates and between fishes were far weaker, with the weakest links of all being the few instances of invertebrates parasitizing fishes. Dynamic modelling simulations that ran for the equivalent of 10 years revealed that fewer species were lost from the more acid food webs than those at high pH, further confirming the suggestion of a negative relationship between stability and pH. This finding, which supports earlier ideas from empirical studies that have considered other types of stability, might account for the limited biological recovery in previously acidified freshwaters that are showing evidence of chemical recovery.

Evidence of chemical recovery from acidification in European freshwaters has emerged in recent years, with many previously damaged systems responding to decades of reduced acidifying emissions. Biological recovery, however, has often lagged behind, and this has been ascribed to several possible mechanisms, including inertia in the food web. We examined two decades of change in hindcasted food webs for Lochnagar, a Scottish mountain lake, to make inferences about the potential dynamical stability of the system and to assess the prospects for future biological recovery. Although community composition tracked temporal changes in acidity, this was neither sustained nor directional, and mainly manifested as shifts in relative abundances rather than the establishment of more acid‐sensitive species. The food web was highly interconnected and reticulate, especially in years when species richness was low, and subsidized by external inputs of detritus. Among the primary consumers, generalist herbivore–detritivores maintained feeding links with the scant algal resources, which appeared insufficient to support viable populations of specialist grazers. Together, these characteristics, which are shared with many other acidified freshwaters, are likely to make the community dynamically stable and resistant to invasions of potential new colonists, thereby slowing the pace of future biological recovery.

Recent attempts to include more ecological detail in connectance food webs have revealed strong relationships between food web structure, species abundance and body size. Few studies, however, have assessed these and other macroecological patterns in food webs in order to examine how network structure, dynamics and their determinants change across environmental gradients. Here, we present 20 highly resolved, standardized stream food webs along a wide pH gradient (5.0–8.4). Our main goal of this study was to assess the influence of external environmental and internal biotic influences on community structure and stability. Many structural features of the food webs changed across the gradient, with web size, linkage density and complexity all increasing with pH. Chlorophyll-a concentrations in epilithic biofilms, as well as the biomass of macroinvertebrates and fish, were also positively correlated with pH. Directed connectance was not correlated with pH in our study, however, although some of the smallest food webs at the lowest pH displayed the highest connectance amongst the networks in this data set. The prevalence of generalism in such food webs, with many alternative food chains passing through any given species, might serve to confer a degree of stability upon these networks, if most feeding links are weak. We found clear differences between our allometrically inferred measures of per capita interaction strengths within the food web, with particularly strong links existing between herbivores and their algal resources and between fish and invertebrates, both of which also became more prevalent at high pH. Predatory interactions between invertebrates and between fishes were far weaker, with the weakest links of all being the few instances of invertebrates parasitizing fishes. Dynamic modelling simulations that ran for the equivalent of 10 years revealed that fewer species were lost from the more acid food webs than those at high pH, further confirming the suggestion of a negative relationship between stability and pH. This finding, which supports earlier ideas from empirical studies that have considered other types of stability, might account for the limited biological recovery in previously acidified freshwaters that are showing evidence of chemical recovery.

Ecological networks are typically complex constructions of species and their interactions. During the last decade, the study of networks has moved from static to dynamic analyses, and has attained a deeper insight into their internal structure, heterogeneity, and temporal and spatial resolution. Here, we review, discuss and suggest research lines in the study of the spatio-temporal heterogeneity of networks and their hierarchical nature. We use case study data from two well-characterized model systems (the food web in Broadstone Stream in England and the pollination network at Zackenberg in Greenland), which are complemented with additional information from other studies. We focus upon eight topics: temporal dynamic space-for-time substitutions linkage constraints habitat borders network modularity individual-based networks invasions of networks and super networks that integrate different network types. Few studies have explicitly examined temporal change in networks, and we present examples that span from daily to decadal change: a common pattern that we see is a stable core surrounded by a group of dynamic, peripheral species, which, in pollinator networks enter the web via preferential linkage to the most generalist species. To some extent, temporal and spatial scales are interchangeable (i.e. networks exhibit 'ergodicity') and we explore how space-for-time substitutions can be used in the study of networks. Network structure is commonly constrained by phenological uncoupling (a temporal phenomenon), abundance, body size and population structure. Some potential links are never observed, that is they are 'forbidden' (fully constrained) or 'missing' (a sampling effect), and their absence can be just as ecologically significant as their presence. Spatial habitat borders can add heterogeneity to network structure, but their importance has rarely been studied: we explore how habitat generalization can be related to other resource dimensions. Many networks are hierarchically structured, with modules forming the basic building blocks, which can result in self-similarity. Scaling down from networks of species reveals another, finer-grained level of individual-based organization, the ecological consequences of which have yet to be fully explored. The few studies of individual-based ecological networks that are available suggest the potential for large intraspecific variance and, in the case of food webs, strong size-structuring. However, such data are still scarce and more studies are required to link individual-level and species-level networks. Invasions by alien species can be tracked by following the topological 'career' of the invader as it establishes itself within a network, with potentially important implications for conservation biology. Finally, by scaling up to a higher level of organization, it is possible to combine different network types (e.g. food webs and mutualistic networks) to form super networks, and this new approach has yet to be integrated into mainstream ecological research. We conclude by listing a set of research topics that we see as emerging candidates for ecological network studies in the near future.