ArticleScientific reports2017
Ecological Network Inference From Long-Term Presence-Absence Data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Wind conditions shape co-migration fidelity in trans-Saharan birds at a Mediterranean stopover site.Royal Society open science · 2026Article
- Construction of a potential ecological network based on public datasets: a case study in Tuscany.Data in brief · 2026Article
- Unifying microorganisms and macrograzers in intertidal rocky shore ecological networks.Ecology · 2026Article
- Bayesian networks for network inference in biology.Journal of the Royal Society, Interface · 2025Review
- Co-migration fidelity at a stopover site increases over time in African-European migratory landbirds.Royal Society open science · 2023Article
- Network inference from short, noisy, low time-resolution, partial measurements: Application toProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Complexity-stability trade-off in empirical microbial ecosystems.Nature ecology & evolution · 2022Article
- A roadmap towards predicting species interaction networks (across space and time).Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny.PLoS biology · 2020Article
- Should ecologists prefer model- over distance-based multivariate methods?Ecology and evolution · 2020Article
- Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge.BMC ecology · 2020Article
- How sample heterogeneity can obscure the signal of microbial interactions.The ISME journal · 2019Review
- Ecological Network Inference From Long-Term Presence-Absence Data.Scientific reports · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ecological communities are characterized by complex networks of trophic and nontrophic interactions, which shape the dy-namics of the community. Machine learning and correlational methods are increasingly popular for inferring networks from co-occurrence and time series data, particularly in microbial systems. In this study, we test the suitability of these methods for inferring ecological interactions by constructing networks using Dynamic Bayesian Networks, Lasso regression, and Pear-son's correlation coefficient, then comparing the model networks to empirical trophic and nontrophic webs in two ecological systems. We find that although each model significantly replicates the structure of at least one empirical network, no model significantly predicts network structure in both systems, and no model is clearly superior to the others. We also find that networks inferred for the Tatoosh intertidal match the nontrophic network much more closely than the trophic one, possibly due to the challenges of identifying trophic interactions from presence-absence data. Our findings suggest that although these methods hold some promise for ecological network inference, presence-absence data does not provide enough signal for models to consistently identify interactions, and networks inferred from these data should be interpreted with caution.
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Registered trials
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