<scp>NetworkExtinction</scp>: An R package to simulate extinction propagation and rewiring potential in ecological networks

Ávila‐Thieme, M. Isidora; Kusch, Erik; Corcoran, Derek; Castillo, Simon P.; Valdovinos, Fernanda S.; Navarrete, Sergio A.; Marquet, Pablo A.

doi:10.1111/2041-210x.14126

Cited by 6 publications

(6 citation statements)

References 65 publications

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“…To investigate the potential for secondary extinctions of vertebrates (where the loss of one species leads to the losses of others), we utilized the NetworkExtinctions package in R (Ávila‐Thieme et al., 2023), which is based on methods originally proposed by Dunne and Williams (2009). The method involves removal of a primary species from the network, followed by a review of the resources remaining for the remaining species.…”

Section: Methodsmentioning

confidence: 99%

Potential extinction cascades in a desert ecosystem: Linking food web interactions to community viability

Eichenwald,

Fefferman,

Reed

2024

Ecology and Evolution

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Desert communities are threatened with species loss due to climate change, and their resistance to such losses is unknown. We constructed a food web of the Mojave Desert terrestrial community (300 nodes, 4080 edges) to empirically examine the potential cascading effects of bird extinctions on this desert network, compared to losses of mammals and lizards. We focused on birds because they are already disappearing from the Mojave, and their relative thermal vulnerabilities are known. We quantified bottom‐up secondary extinctions and evaluated the relative resistance of the community to losses of each vertebrate group. The impact of random bird species loss was relatively low compared to the consequences of mammal (causing the greatest number of cascading losses) or reptile loss, and birds were relatively less likely to be in trophic positions that could drive top‐down effects in apparent competition and tri‐tropic cascade motifs. An avian extinction cascade with year‐long resident birds caused more secondary extinctions than the cascade involving all bird species for randomized ordered extinctions. Notably, we also found that relatively high interconnectivity among avian species has formed a subweb, enhancing network resistance to bird losses.

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Section: Methodsmentioning

confidence: 99%

Potential extinction cascades in a desert ecosystem: Linking food web interactions to community viability

Eichenwald,

Fefferman,

Reed

2024

Ecology and Evolution

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“…When encoding ecological networks, it is common practice to represent nodes (i.e., species) and their links (i.e., interactions or associations) as matrices (Ávila-Thieme et al, 2023; Opedal & Hegland, 2020). Within these matrices, columns and rows represent species-identities while cells contain the link weight (interaction/association strength) between corresponding species pairs.…”

Section: Methodsmentioning

confidence: 99%

A Novel Simulation Framework for Validation of Ecological Network Inference

Kusch

Vinton

2023

Preprint

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1. Understanding how the differential magnitude and sign of ecological interactions vary across space is vital to assessing ecosystem resilience to biodiversity loss and predict community assemblies. This necessity for ecological network knowledge and their labour-intensive sampling requirements has spurred the creation of ecological network inference methodology. Recent research has identified inconsistencies in networks inferred using different approaches thus necessitating quantification of inference performance to facilitate choice of network inference approach. 2. Here we develop a data simulation method to generate data products fit for network inference and subsequently quantify the validity of two well-established ecological interaction network inference methods - HMSC and COOCCUR. The simulation framework we present here can be parameterised using real-world information (e.g., biological interactions observed in-situ and bioclimatic niche preferences) thus representing network inference capabilities in real-world applications. Using this framework, it is thus possible to evaluate the performance of any ecological network inference approach. 3. We find that network inference performance scores highlight concerningly low accuracy of inferred networks as compared to true association networks and suggest analysis procedures with which to explore network inference reliability with respect to bioclimatic niche preferences and association strength of association partner-species. 4. With this study, we provide the groundwork with which to validate and compare ecological network inference methods, and ultimately vastly increase our ability to predict species biodiversity across space.

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“…2010 ; Baldock et al . 2019 ) and different loss patterns and rewiring potentials ( Ávila-Thieme et al . 2023 ).…”

Section: Stability In Plant–pollinator Community Studies: a Systemati...mentioning

confidence: 99%

Stability in plant–pollinator communities across organizational levels: present, gaps, and future

Magrach,

Montoya

2024

AoB PLANTS

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The study of ecological stability continues to fill the pages of scientific journals almost seven decades after the first ecologists initiated this line of research. The many advances in this field have focused on understanding the stability of populations, communities or functions within single guilds or trophic levels, with less research conducted across multiple trophic levels and considering the different interactions that relate species to each other. Here, we review the recent literature on the multiple dimensions of ecological stability specifically within plant-pollinator communities. We then focus on one of stability´s dimensions, temporal invariability, and adapt an existing partitioning framework that bridges invariability and synchrony measures across spatial scales and organizational levels to accommodate interactions between plants and their pollinators. Finally, we use this framework to analyze temporal invariability in plant reproductive success, partitioning it on invariability and synchrony components across plant and pollinator populations and communities, as well as their interactions, using a well-resolved dataset that encompasses data for two years. Our review of the literature points to several significant gaps in our current knowledge, with simulation studies clearly overrepresented in the literature as opposed to experimental or empirical approaches. Our quantitative approach to partitioning invariability shows similar patterns of decreasing temporal invariability across increasing organizational levels driven by asynchronous dynamics amongst populations and communities, which overall stabilize ecosystem functioning (plant reproductive success). This study represents a first step towards a better comprehension of temporal invariability in ecosystem functions defined by interactions between species and provides a blueprint for the type of spatially replicated multi-year data that needs to be collected in the future to further our understanding of ecological stability within multi-trophic communities.

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NetworkExtinction: An R package to simulate extinction propagation and rewiring potential in ecological networks

Cited by 6 publications

References 65 publications

Potential extinction cascades in a desert ecosystem: Linking food web interactions to community viability

Potential extinction cascades in a desert ecosystem: Linking food web interactions to community viability

A Novel Simulation Framework for Validation of Ecological Network Inference

Stability in plant–pollinator communities across organizational levels: present, gaps, and future

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