scholarly journals fluxweb: a R package to easily estimate energy fluxes in food webs

2017 ◽  
Author(s):  
Benoit Gauzens ◽  
Andrew Barnes ◽  
Darren Giling ◽  
Jes Hines ◽  
Malte Jochum ◽  
...  
Keyword(s):  
Steady State ◽  
Food Web ◽  
Food Webs ◽  
Ecosystem Functioning ◽  
R Package ◽  
Estimation Methods ◽  
List Type ◽  
Energy Fluxes ◽  
Flux System ◽  
Primary Output

AbstractUnderstanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food-web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remains problematic because current methods become unmanageable as network complexity increases.We developed a generalisation of previous indirect estimation methods assuming a steady state system [1, 2, 3]: the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node’s losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://bit.ly/2OC0uKF).We also present how the framework can merge with the allometric theory of ecology [4] to calculate fluxes based on easily obtainable organism-level data (i.e. body masses and species groups -eg, plants animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production.The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g. predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state.Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food-web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.

scholarly journals NetworkExtinction: an R package to explore the propagation of extinctions through complex ecological networks

2020 ◽  
Author(s):  
M. Isidora Ávila-Thieme ◽  
Derek Corcoran ◽  
Simón P. Castillo ◽  
Fernanda S. Valdovinos ◽  
Sergio A. Navarrete ◽  
...  
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Degree Distribution ◽  
Null Model ◽  
Biodiversity Loss ◽  
R Package ◽  
List Type ◽  
Food Web Structure ◽  
Species Extinction ◽  
Species Extinctions

AbstractBiodiversity loss is one of the current drivers of global change with an acute impact on community structure. Different measures and tools (e.g., simulations of extinction events) have been developed to analyze the structure of ecological systems and their stability under biodiversity loss, especially in complex settings with multiple interacting species, such as food webs. However, there remains the need for tools that enable a quick assessment of the ensuing impacts on food webs structure due to species extinction. Here, we develop an R package to explore the propagation of species extinctions through food webs, measured as secondary extinctions, according to user-defined node removal sequences.In the NetworkExtinction package, we seek the integration between theory and computational simulations by developing six functions to analyze and visualize the structure and robustness of food webs represented as binary adjacency matrices. Three functions simulate the sequential extinction of species; a fourth function compares food web metrics between random and non-random extinction sequences; a fifth function visualizes the change in a given network metric along with the steps of sequential species extinction; a sixth function allows the user to fit and visualize the degree distribution of the network, fitting linear and non-linear regressions. We illustrate the package’s use and its outputs by analysing a Chilean coastal marine food web.By using the NetworkExtinction package, the user can estimate the food web robustness after performing species’ extinction routines based on several algorithms. Moreover, the user can compare the number of simulated secondary extinctions against a null model of random extinctions. The visualizations allow graphing topological indexes that the deletion sequences functions calculate after each removal step. Finally, the user can fit the degree distribution of the food web.The NetworkExtinction R package is a compact and easy-to-use package to visualize and assess the food web structure (degree distribution) and robustness to different sequences of species loss. Therefore, this package is particularly useful to evaluate the ecosystem response to anthropogenic and environmental perturbations that produce non-random species extinctions. In that way, it also allows us to assess the contribution of central nodes to food webs stability.

scholarly journals The meaning of functional trait composition of food webs for ecosystem functioning

2016 ◽  
Vol 371 (1694) ◽  
pp. 20150268 ◽  
Author(s):  
Dominique Gravel ◽  
Camille Albouy ◽  
Wilfried Thuiller
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Functional Diversity ◽  
Ecosystem Functioning ◽  
Functional Trait ◽  
Plant Ecology ◽  
Functional Composition ◽  
Top Down ◽  
Bottom Up ◽  
Functional Trait Diversity

There is a growing interest in using trait-based approaches to characterize the functional structure of animal communities. Quantitative methods have been derived mostly for plant ecology, but it is now common to characterize the functional composition of various systems such as soils, coral reefs, pelagic food webs or terrestrial vertebrate communities. With the ever-increasing availability of distribution and trait data, a quantitative method to represent the different roles of animals in a community promise to find generalities that will facilitate cross-system comparisons. There is, however, currently no theory relating the functional composition of food webs to their dynamics and properties. The intuitive interpretation that more functional diversity leads to higher resource exploitation and better ecosystem functioning was brought from plant ecology and does not apply readily to food webs. Here we appraise whether there are interpretable metrics to describe the functional composition of food webs that could foster a better understanding of their structure and functioning. We first distinguish the various roles that traits have on food web topology, resource extraction (bottom-up effects), trophic regulation (top-down effects), and the ability to keep energy and materials within the community. We then discuss positive effects of functional trait diversity on food webs, such as niche construction and bottom-up effects. We follow with a discussion on the negative effects of functional diversity, such as enhanced competition (both exploitation and apparent) and top-down control. Our review reveals that most of our current understanding of the impact of functional trait diversity on food web properties and functioning comes from an over-simplistic representation of network structure with well-defined levels. We, therefore, conclude with propositions for new research avenues for both theoreticians and empiricists.

scholarly journals Loss of functionally unique species may gradually undermine ecosystems

2010 ◽  
Vol 278 (1713) ◽  
pp. 1886-1893 ◽  
Author(s):  
Eoin J. O'Gorman ◽  
Jon M. Yearsley ◽  
Tasman P. Crowe ◽  
Mark C. Emmerson ◽  
Ute Jacob ◽  
...  
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Ecosystem Functioning ◽  
Trophic Position ◽  
Interaction Strength ◽  
Natural Systems ◽  
Interacting Species ◽  
Weakly Interacting ◽  
Taxonomic Groups ◽  
Unique Species

Functionally unique species contribute to the functional diversity of natural systems, often enhancing ecosystem functioning. An abundance of weakly interacting species increases stability in natural systems, suggesting that loss of weakly linked species may reduce stability. Any link between the functional uniqueness of a species and the strength of its interactions in a food web could therefore have simultaneous effects on ecosystem functioning and stability. Here, we analyse patterns in 213 real food webs and show that highly unique species consistently tend to have the weakest mean interaction strength per unit biomass in the system. This relationship is not a simple consequence of the interdependence of both measures on body size and appears to be driven by the empirical pattern of size structuring in aquatic systems and the trophic position of each species in the web. Food web resolution also has an important effect, with aggregation of species into higher taxonomic groups producing a much weaker relationship. Food webs with fewer unique and less weakly interacting species also show significantly greater variability in their levels of primary production. Thus, the loss of highly unique, weakly interacting species may eventually lead to dramatic state changes and unpredictable levels of ecosystem functioning.

scholarly journals Top predators govern multitrophic diversity effects in tritrophic food webs

2020 ◽  
Author(s):  
Ruben Ceulemans ◽  
Christian Guill ◽  
Ursula Gaedke
Keyword(s):  
Temporal Variation ◽  
Food Web ◽  
Food Webs ◽  
Functional Diversity ◽  
Trophic Level ◽  
Ecosystem Functioning ◽  
Initial Conditions ◽  
Trophic Levels ◽  
Natural Food ◽  
Model Parameters

AbstractIt is well known that functional diversity strongly affects ecosystem functioning. However, even in rather simple model communities consisting of only two or, at best, three trophic levels, the relationship between multitrophic functional diversity and ecosystem functioning appears difficult to generalize, due to its high contextuality. In this study, we considered several differently structured tritrophic food webs, in which the amount of functional diversity was varied independently on each trophic level. To achieve generalizable results, largely independent of parametrization, we examined the outcomes of 128, 000 parameter combinations sampled from ecologically plausible intervals, with each tested for 200 randomly sampled initial conditions. Analysis of our data was done by training a Random Forest model. This method enables the identification of complex patterns in the data through partial dependence graphs, and the comparison of the relative influence of model parameters, including the degree of diversity, on food web properties. We found that bottom-up and top-down effects cascade simultaneously throughout the food web, intimately linking the effects of functional diversity of any trophic level to the amount of diversity of other trophic levels, which may explain the difficulty in unifying results from previous studies. Strikingly, only with high diversity throughout the whole food web, different interactions synergize to ensure efficient exploitation of the available nutrients and efficient biomass transfer, ultimately leading to a high biomass and production on the top level. The temporal variation of biomass showed a more complex pattern with increasing multitrophic diversity: while the system initially became less variable, eventually the temporal variation rose again due to the increasingly complex dynamical patterns. Importantly, top predator diversity and food web parameters affecting the top trophic level were of highest importance to determine the biomass and temporal variability of any trophic level. Overall, our study reveals that the mechanisms by which diversity influences ecosystem functioning are affected by every part of the food web, hampering the extrapolation of insights from simple monotrophic or bitrophic systems to complex natural food webs.

scholarly journals Multifunctionality of belowground food webs: resource, size and spatial energy channels

2021 ◽  
Author(s):  
Anton M. Potapov
Keyword(s):  
Organic Matter ◽  
Food Web ◽  
Food Webs ◽  
Terrestrial Ecosystems ◽  
Feeding Preference ◽  
Size Spectrum ◽  
Soil Food Web ◽  
Energy Fluxes ◽  
Biogeochemical Models ◽  
Web Reconstruction

The belowground compartment of terrestrial ecosystems drives nutrient cycling, the decomposition and stabilisation of organic matter, and supports aboveground life. Belowground consumers create complex food webs that regulate functioning, ensure stability and support biodiversity both below and above ground. However, existing soil food-web reconstructions do not match recently accumulated empirical evidence and there is no comprehensive reproducible approach that accounts for the complex resource, size and spatial structure of food webs in soil. Here I build on generic food-web organization principles and use multifunctional classification of soil protists, invertebrates and vertebrates, to reconstruct "multichannel" food-web across size classes of soil-associated consumers. This reconstruction is based on overlying feeding preference, prey protection, size spectrum and spatial distribution matrices combined with biomasses of trophic guilds to infer weighted trophic interactions. I then use food-web reconstruction, together with assimilation efficiencies, to calculate energy fluxes assuming a steady-state energetic system. Based on energy fluxes, I describe a number of indicators, related to stability, biodiversity and multiple ecosystem-level functions such as herbivory, top-down control, translocation and transformation of organic matter. I illustrate the approach with an empirical example, comparing it with traditional resource-focused soil food-web reconstruction. The multichannel reconstruction can be used to assess trophic multifunctionality (analogous to ecosystem multifunctionality), i.e. simultaneous support of multiple trophic functions by the food-web, and compare it across communities and ecosystems spanning beyond the soil. With further validation and parametrization, my multichannel reconstruction approach provides an effective tool for understanding and analysing soil food webs. I believe that having this tool will inspire more people to comprehensively describe soil communities and belowground-aboveground interactions. Such studies will provide informative indicators for including consumers as active agents in biogeochemical models, not only locally but also on regional and global scales.

scholarly journals Interplay between the paradox of enrichment and nutrient cycling in food webs

2018 ◽  
Author(s):  
Pierre Quévreux ◽  
Sébastien Barot ◽  
Élisa Thébault
Keyword(s):  
Nutrient Cycling ◽  
Food Web ◽  
Food Webs ◽  
Trophic Level ◽  
Temporal Variability ◽  
Ecosystem Functioning ◽  
Nutrient Inputs ◽  
Primary Producers ◽  
Paradox Of Enrichment ◽  
Food Web Dynamics

AbstractNutrient cycling is fundamental to ecosystem functioning. Despite recent major advances in the understanding of complex food web dynamics, food web models have so far generally ignored nutrient cycling. However, nutrient cycling is expected to strongly impact food web stability and functioning. To make up for this gap, we built an allometric and size structured food web model including nutrient cycling. By releasing mineral nutrients, recycling increases the availability of limiting resources for primary producers and links each trophic level to the bottom of food webs. We found that nutrient cycling can provide a significant part of the total nutrient supply of the food web, leading to a strong enrichment effect that promotes species persistence in nutrient poor ecosystems but leads to a paradox of enrichment at high nutrient inputs. The presence of recycling loops linking each trophic level to the basal resources weakly affects species biomass temporal variability in the food web. Recycling loops tend to slightly dampen the destabilising effect of nutrient enrichment on consumer temporal variability while they have opposite effects for primary producers. By considering nutrient cycling, this new model improves our understanding of the response of food webs to nutrient availability and opens perspectives to better link studies on food web dynamics and ecosystem functioning.

scholarly journals Seasonal food webs with migrations: multi-season models reveal indirect species interactions in the Canadian Arctic tundra

2020 ◽  
Vol 378 (2181) ◽  
pp. 20190354 ◽  
Author(s):  
Chantal Hutchison ◽  
Frédéric Guichard ◽  
Pierre Legagneux ◽  
Gilles Gauthier ◽  
Joël Bêty ◽  
...  
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Ecosystem Functioning ◽  
Species Interactions ◽  
Multiple Equilibria ◽  
Community Dynamics ◽  
Static Model ◽  
Predator Prey ◽  
Summer Time ◽  
The Impact

Models incorporating seasonality are necessary to fully assess the impact of global warming on Arctic communities. Seasonal migrations are a key component of Arctic food webs that still elude current theories predicting a single community equilibrium. We develop a multi-season model of predator–prey dynamics using a hybrid dynamical systems framework applied to a simplified tundra food web (lemming–fox–goose–owl). Hybrid systems models can accommodate multiple equilibria, which is a basic requirement for modelling food webs whose topology changes with season. We demonstrate that our model can generate multi-annual cycling in lemming dynamics, solely from a combined effect of seasonality and state-dependent behaviour. We compare our multi-season model to a static model of the predator–prey community dynamics and study the interactions between species. Interestingly, including seasonality reveals indirect interactions between migrants and residents not captured by the static model. Further, we find that the direction and magnitude of interactions between two species are not necessarily accurate using only summer time-series. Our study demonstrates the need for the development of multi-season models and provides the tools to analyse them. Integrating seasonality in food web modelling is a vital step to improve predictions about the impacts of climate change on ecosystem functioning. This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning’.

scholarly journals Mechanisms of trophic niche compression: evidence from landscape disturbance

2018 ◽  
Author(s):  
Francis J. Burdon ◽  
Angus R. McIntosh ◽  
Jon S. Harding
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Agricultural Land ◽  
Trophic Position ◽  
Resource Scarcity ◽  
Trophic Niche ◽  
Isotopic Niche ◽  
List Type ◽  
Landscape Disturbance ◽  
Trophic Diversity

AbstractNatural and anthropogenic disturbances commonly alter patterns of biodiversity and ecosystem functioning. However, how food webs respond to these changes remains poorly understood. Here, we have described aquatic food webs using invertebrate and fish community composition, functional traits, and stable isotopes from twelve agricultural streams along a landscape disturbance gradient.We predicted that excessive inputs of fine inorganic sediment (sedimentation) associated with agricultural land uses would negatively influence stream trophic diversity (e.g., reduced vertical and horizontal trophic niche breadths).Food-web properties based on Bayesian analyses of stable isotope data (δ13C and δ15N) from consumers showed that increasing sediment disturbance was associated with reduced trophic diversity, indicated by the whole community (fish and invertebrates combined) occupying a smaller area in isotopic niche space. Reductions in trophic diversity were best explained by a narrowing of the consumer δ13C range, and to a lesser extent, consumer δ15N range along the sedimentation gradient.We hypothesized that multiple mechanisms associated with sedimentation may have caused trophic niche ‘compression’. Decreased niche partitioning, driven by increasing habitat homogeneity, environmental filtering, and resource scarcity seemingly lead to a greater similarity in trophic roles. These pathways may have contributed to a reduction in trophic diversity, whereas increased resource homogeneity was seemingly less important.Our results also indicate downward shifts in the vertical trophic position of benthic meospredators and invertebrate prey relative to higher consumers. This ‘trophic decoupling’ suggests that terrestrial resource subsidies may offset reductions of aquatic prey for larger stream fishes.Sedimentation was associated with reduced trophic diversity, which may affect the functioning and stability of stream ecosystems. Our study helps explain how multiple mechanisms can influence food-web properties in response to this type of disturbance.

scholarly journals Ecological Network assembly: how the regional metaweb influences local food webs

2018 ◽  
Author(s):  
Leonardo A. Saravia ◽  
Tomás I. Marina ◽  
Marleen De Troch ◽  
Fernando R. Momo
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Local Food ◽  
Weddell Sea ◽  
List Type ◽  
Assembly Model ◽  
Ecological Stability ◽  
Food Web Structure ◽  
Potter Cove ◽  
Global Properties

AbstractLocal food webs can be studied as the realisation of a sequence of colonising and extinction events, where a regional pool of species — called the metaweb— acts as a source for new species. Food webs are thus the result of assembly processes that are influenced by migration, habitat filtering, stochastic factors, and dynamical constraints. Therefore, we expect their structure to reflect the action of these influences.We compared the structure of empirical local food webs to (1) a metaweb, (2) randomly-constructed webs, and (3) webs resulting from an assembly model. The assembly model had no population dynamics but simply required that consumer species have at least one prey present in the local web. We compared global properties, network sub-structures—motifs— and topological roles that are node-level properties. We hypothesised that the structure of empirical food webs should differ from other webs in a way that reflected dynamical stability and other local constraints. Three data-sets were used: (1) the marine Antarctic metaweb, built using a dietary database; (2) the Weddell Sea local food web; and (3) the Potter Cove local food web.Contrary to our expectation, we found that, while most network global properties of empirical webs were different from random webs, there were almost no differences between empirical webs and those resulting from the assembly model. Further, while empirical webs showed different motif representations compared to the assembly model, these were not motifs associated with increased stability. Species’ topological roles showed differences between the metaweb and local food webs that were not explained by the assembly model, suggesting that species in empirical webs are selected by habitat or dispersal limitations.Our results suggest that there is not a strong dynamical restriction upon food web structure that operates at local scales. Instead, the structure of local webs is inherited from the metaweb with modifications imposed by local habitats.Recently, it has been found in competitive and mutualistic networks that structures that are often attributed as causes or consequences of ecological stability are probably a by-product of the assembly processes (i.e. spandrels). We extended these results to trophic networks suggesting that this could be a more general phenomenon.

scholarly journals fluxweb : An R package to easily estimate energy fluxes in food webs

2018 ◽  
Vol 10 (2) ◽  
pp. 270-279 ◽  
Author(s):  
Benoit Gauzens ◽  
Andrew Barnes ◽  
Darren P. Giling ◽  
Jes Hines ◽  
Malte Jochum ◽  
...  
Keyword(s):  
Food Webs ◽  
R Package ◽  
Energy Fluxes
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