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 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 Food web persistence in fragmented landscapes

2017 ◽  
Vol 284 (1859) ◽  
pp. 20170350 ◽  
Author(s):  
Jinbao Liao ◽  
Daniel Bearup ◽  
Bernd Blasius
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Trophic Position ◽  
Biodiversity Loss ◽  
Habitat Destruction ◽  
Trophic Levels ◽  
Food Web Structure ◽  
Spatially Extended ◽  
Biodiversity Maintenance ◽  
Patch Connectivity

Habitat destruction, characterized by patch loss and fragmentation, is a key driver of biodiversity loss. There has been some progress in the theory of spatial food webs; however, to date, practically nothing is known about how patch configurational fragmentation influences multi-trophic food web dynamics. We develop a spatially extended patch-dynamic model for different food webs by linking patch connectivity with trophic-dependent dispersal (i.e. higher trophic levels displaying longer-range dispersal). Using this model, we find that species display different sensitivities to patch loss and fragmentation, depending on their trophic position and the overall food web structure. Relative to other food webs, omnivory structure significantly increases system robustness to habitat destruction, as feeding on different trophic levels increases the omnivore's persistence. Additionally, in food webs with a dispersal–competition trade-off between species, intermediate levels of habitat destruction can enhance biodiversity by creating refuges for the weaker competitor. This demonstrates that maximizing patch connectivity is not always effective for biodiversity maintenance, as in food webs containing indirect competition, doing so may lead to further species loss.

scholarly journals Cascading extinctions and community collapse in model food webs

2009 ◽  
Vol 364 (1524) ◽  
pp. 1711-1723 ◽  
Author(s):  
Jennifer A. Dunne ◽  
Richard J. Williams
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Species Interactions ◽  
Structural Integrity ◽  
Null Model ◽  
Realistic Model ◽  
Species Loss ◽  
Food Web Structure ◽  
As Species ◽  
Model Food

Species loss in ecosystems can lead to secondary extinctions as a result of consumer–resource relationships and other species interactions. We compare levels of secondary extinctions in communities generated by four structural food-web models and a fifth null model in response to sequential primary species removals. We focus on various aspects of food-web structural integrity including robustness, community collapse and threshold periods, and how these features relate to assumptions underlying different models, different species loss sequences and simple measures of diversity and complexity. Hierarchical feeding, a fundamental characteristic of food-web structure, appears to impose a cost in terms of robustness and other aspects of structural integrity. However, exponential-type link distributions, also characteristic of more realistic models, generally confer greater structural robustness than the less skewed link distributions of less realistic models. In most cases for the more realistic models, increased robustness and decreased levels of web collapse are associated with increased diversity, measured as species richness S , and increased complexity, measured as connectance C . These and other results, including a surprising sensitivity of more realistic model food webs to loss of species with few links to other species, are compared with prior work based on empirical food-web data.

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 Landscape heterogeneity buffers biodiversity of simulated meta-food-webs under global change through rescue and drainage effects

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Remo Ryser ◽  
Myriam R. Hirt ◽  
Johanna Häussler ◽  
Dominique Gravel ◽  
Ulrich Brose
Keyword(s):  
Habitat Fragmentation ◽  
Food Web ◽  
Food Webs ◽  
Landscape Heterogeneity ◽  
Landscape Connectivity ◽  
Biodiversity Loss ◽  
Mechanistic Explanation ◽  
Population Densities ◽  
Rescue Effect ◽  
Drainage Effect

AbstractHabitat fragmentation and eutrophication have strong impacts on biodiversity. Metacommunity research demonstrated that reduction in landscape connectivity may cause biodiversity loss in fragmented landscapes. Food-web research addressed how eutrophication can cause local biodiversity declines. However, there is very limited understanding of their cumulative impacts as they could amplify or cancel each other. Our simulations of meta-food-webs show that dispersal and trophic processes interact through two complementary mechanisms. First, the ‘rescue effect’ maintains local biodiversity by rapid recolonization after a local crash in population densities. Second, the ‘drainage effect’ stabilizes biodiversity by preventing overshooting of population densities on eutrophic patches. In complex food webs on large spatial networks of habitat patches, these effects yield systematically higher biodiversity in heterogeneous than in homogeneous landscapes. Our meta-food-web approach reveals a strong interaction between habitat fragmentation and eutrophication and provides a mechanistic explanation of how landscape heterogeneity promotes biodiversity.

scholarly journals The more food webs change, the more they stay the same

2009 ◽  
Vol 364 (1524) ◽  
pp. 1789-1801 ◽  
Author(s):  
Kevin Shear McCann ◽  
Neil Rooney
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Temporal Variability ◽  
Spatial And Temporal Variability ◽  
Scale Invariant ◽  
Food Web Structure ◽  
Behavioural Responses ◽  
Web Structure ◽  
Food Web Ecology ◽  
Food Web Theory

Here, we synthesize a number of recent empirical and theoretical papers to argue that food-web dynamics are characterized by high amounts of spatial and temporal variability and that organisms respond predictably, via behaviour, to these changing conditions. Such behavioural responses on the landscape drive a highly adaptive food-web structure in space and time. Empirical evidence suggests that underlying attributes of food webs are potentially scale-invariant such that food webs are characterized by hump-shaped trophic structures with fast and slow pathways that repeat at different resolutions within the food web. We place these empirical patterns within the context of recent food-web theory to show that adaptable food-web structure confers stability to an assemblage of interacting organisms in a variable world. Finally, we show that recent food-web analyses agree with two of the major predictions of this theory. We argue that the next major frontier in food-web theory and applied food-web ecology must consider the influence of variability on food-web structure.

Functional diversity alters the effects of a pulse perturbation on the dynamics of tritrophic food webs

2021 ◽  
Author(s):  
Ruben Ceulemans ◽  
Laurie Anne Myriam Wojcik ◽  
Ursula Gaedke
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Functional Diversity ◽  
Feedback Loop ◽  
Environmental Changes ◽  
Biodiversity Loss ◽  
Trophic Levels ◽  
Nutrient Pulse ◽  
Trade Offs ◽  
Food Web Model

Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of climate and human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. Here, we investigate the effects of a nutrient pulse on the resistance, resilience and elasticity of a tritrophic---and thus more realistic---plankton food web model depending on its functional diversity. We compare a non-adaptive food chain with no diversity to a highly diverse food web with three adaptive trophic levels. The species fitness differences are balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occured. Importantly, we found that a more diverse food web was generally more resistant, resilient, and elastic. Particularly, functional diversity dampened the probability of a regime shift towards a non-desirable alternative state. In addition, despite the complex influence of the shape and type of the dynamical attractors, the basal-intermediate interaction determined the robustness against a nutrient pulse. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and elasticity as functional diversity declines.

scholarly journals The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 603-628 ◽  
Author(s):  
Tomas Roslin ◽  
Sanna Majaneva
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Taxonomic Resolution ◽  
Dna Barcodes ◽  
Food Web Structure ◽  
Web Studies ◽  
Web Structure ◽  
Asking Questions ◽  
Web Construction ◽  
Interaction Webs

By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems—revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.

scholarly journals Untangling the roles of parasites in food webs with generative network models

2015 ◽  
Author(s):  
Abigail Z. Jacobs ◽  
Jennifer A. Dunne ◽  
Cristopher Moore ◽  
Aaron Clauset
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Statistical Physics ◽  
Network Models ◽  
Food Web Structure ◽  
Free Living ◽  
Web Structure ◽  
Living Species ◽  
Parasitic Interactions ◽  
The Impact

Food webs represent the set of consumer-resource interactions among a set of species that co-occur in a habitat, but most food web studies have omitted parasites and their interactions. Recent studies have provided conflicting evidence on whether including parasites changes food web structure, with some suggesting that parasitic interactions are structurally distinct from those among free-living species while others claim the opposite. Here, we describe a principled method for understanding food web structure that combines an efficient optimization algorithm from statistical physics called parallel tempering with a probabilistic generalization of the empirically well-supported food web niche model. This generative model approach allows us to rigorously estimate the degree to which interactions that involve parasites are statistically distinguishable from interactions among free-living species, whether parasite niches behave similarly to free-living niches, and the degree to which existing hypotheses about food web structure are naturally recovered. We apply this method to the well-studied Flensburg Fjord food web and show that while predation on parasites, concomitant predation of parasites, and parasitic intraguild trophic interactions are largely indistinguishable from free-living predation interactions, parasite-host interactions are different. These results provide a powerful new tool for evaluating the impact of classes of species and interactions on food web structure to shed new light on the roles of parasites in food webs.

scholarly journals Mesoscale variations in the assemblage structure and trophodynamics of mesozooplankton communities of the Adriatic basin (Mediterranean Sea)

2021 ◽  
Author(s):  
Emanuela Fanelli ◽  
Samuele Menicucci ◽  
Sara Malavolti ◽  
Andrea De Felice ◽  
Iole Leonori
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Mediterranean Sea ◽  
Environmental Variables ◽  
Complex Structure ◽  
Assemblage Structure ◽  
Trophic Levels ◽  
Ecosystem Functions ◽  
Food Web Structure ◽  
Adriatic Basin

Abstract. Zooplankton are critical to the functioning of ocean food webs because of their utter abundance and vital ecosystem roles. Zooplankton communities are highly diverse and thus perform a variety of ecosystem functions, thus changes in their community or food web structure may provide evidence of ecosystem alteration. Assemblage structure and trophodynamics of mesozooplantkon communities were examined across the Adriatic basin, the northernmost and most productive basin of the Mediterranean Sea. Samples were collected in June–July 2019 along coast-offshore transects covering the whole western Adriatic side, consistently environmental variables were also recorded. Results showed a clear separation between samples from the northern-central Adriatic and the southern ones, with a further segregation, although less clear, of inshore vs. off-shore stations, the latter mostly dominated in the central and southern stations by gelatinous plankton. Such patterns were mainly driven by chlorophyll-a concentration (as a proxy of primary production) for northern-central stations, i.e. closer to the Po river input, and by temperature and salinity, for southern ones, with the DistLM model explaining 46 % of total variance. The analysis of stable isotopes of nitrogen and carbon allowed to identify a complex food web characterized by 3 trophic levels from herbivores to carnivores, passing through the mixed feeding behavior of omnivores, shifting from phytoplankton/detritus ingestion to microzooplankton. Trophic structure also spatially varied according to sub-area, with the northern-central sub-areas differing from each other and from the southern stations. Our results highlighted the importance of environmental variables as drivers of zooplanktonic communities and the complex structure of their food webs. Disentangling and considering such complexity is crucial to generate realistic predictions on the functioning of aquatic ecosystems, especially in high productive and, at the same time, overexploited area such as the Adriatic Sea.

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