The probabilistic niche model reveals the niche structure and role of body size in a complex food web.
Open accessAbstract
The niche model has been widely used to model the structure of complex food webs, and yet the ecological meaning of the single niche dimension has not been explored. In the niche model, each species has three traits, niche position, diet position and feeding range. Here, a new probabilistic niche model, which allows the maximum likelihood set of trait values to be estimated for each species, is applied to the food web of the Benguela fishery. We also developed the allometric niche model, in which body size is used as the niche dimension. About 80% of the links in the empirical data are predicted by the probabilistic niche model, a significant improvement over recent models. As in the niche model, species are uniformly distributed on the niche axis. Feeding ranges are exponentially distributed, but diet positions are not uniformly distributed below the predator. Species traits are strongly correlated with body size, but the allometric niche model performs significantly worse than the probabilistic niche model. The best-fit parameter set provides a significantly better model of the structure of the Benguela food web than was previously available. The methodology allows the identification of a number of taxa that stand out as outliers either in the model's poor performance at predicting their predators or prey or in their parameter values. While important, body size alone does not explain the structure of the one-dimensional niche.
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“In network inference, there are only a few examples of complete Bayesian models [25,26] and a few examples of MCMC for maximum-likelihood inference [27,28], but Bayesian inference in phylogenetics has been long established [29,30], and provides a clear methodological analogue.”
BackgroundMethod
- Authors
- Williams, R. J., Anandanadesan, A., & Purves, D.
- Affiliations
- Microsoft Research (United Kingdom) (GB)
- Corresponding author
- Williams, Richard J.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-08-09
- Volume
- 5
- Issue
- 8
- Pages
- e12092
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2918514
- OpenAlex
- W2090166751
- Cited by
- 117
- References
- 39
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 6 · 2023: 7 · 2022: 6 · 2021: 7 · 2020: 6 · 2019: 4 · 2018: 6 · 2017: 8 · 2016: 11 · 2015: 7 · 2014: 14 · 2013: 10 · 2012: 9
- FWCI
- 8.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Microsoft Research
- Topics
- Physical Sciences › Environmental Science › Ecology › Isotope Analysis in Ecology
- Physical Sciences › Environmental Science › Global and Planetary Change › Marine and fisheries research
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mathematical and Theoretical Epidemiology and Ecology Models
- Keywords
- food web structure, body size, foraging range, species traits, maximum likelihood estimation
- MeSH terms
- Animals, Predatory Behavior, Stochastic Processes, Models, Statistical, Food Chain, Body Size
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