Weak trophic position-body mass relationships undermine simple size spectrum models for coral reefs
Data files
Dec 17, 2025 version files 8.23 MB
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all_isotopes_DN_BM.csv
306.75 KB
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Analyses_Figures_2025.Rmd
31.14 KB
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DN_individual.csv
3.78 MB
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README.md
4.44 KB
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S3_Table.csv
1.24 MB
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Tpos.csv
2.86 MB
Abstract
Unravelling food web dynamics across biological communities is a central goal of ecology. In size-structured ecosystems, the shape of trophic pyramids is often inferred from the distribution of biomass across body-mass classes, i.e. its size spectrum. Size-spectrum analysis has become a popular tool to study the ecosystem functioning of aquatic ecosystems, including highly diverse coral reefs. However, the key assumption behind size spectra, i.e. that body size directly and positively correlates with trophic position, has rarely been directly evaluated in these systems. Here, we test this assumption by quantifying body mass, population densities and estimating trophic position from stable isotopes for 325 fish species across four Indo-Pacific locations. Consistent with prior studies, we found a positive relationship between biomass and body mass. However, weak and variable relationships between body mass and trophic position led higher biomass in primary consumers than in predators, as expected in traditional bottom-heavy or diamond-shaped trophic structures. Our findings thus challenge previous reports of coral reef fish biomass prevalence in higher trophic levels (e.g., inverted biomass pyramids), suggesting that simple size spectrum models do not adequately represent the trophic structure of reef fish communities.
https://doi.org/10.5061/dryad.tmpg4f58c
Description of the data and file structure
This folder is composed of one .Rmd file and five datasets, including three .xlsx files and two .csv files.
The .Rmd file is called Analyses&Figures.Rmd
It contains the code to produce all of the figures of the corresponding manuscript except figure 1 (theoretical framework) and figure 2 (sampling maps). It uses all five datasets provided.
The code also produces the model results displayed in the Supplementary Tables T1 to T2.
The Analyses_Figures_2025.Rmd file is decomposed into six main sections:
- Data and packages uploading
- Biomass ~ Delta Nitrogen analyses and plots
- Biomass ~ Body mass analyses and plots
- Delta Nitrogen ~ Body mass analyses and plots
- Fig. 3 and S1 Table construction
- Biomass ratios ~ Delta Nitrogen analyses and plots
Datasets (please find below the variable description in each dataset)
The .csv datasets each correspond to an analysis or a sensitivity analysis:
- Delta 15 Nitrogen from predictions (DN_individual.csv): this dataset is the result of the prediction of Delta N values for each individual of the UVC data, based on body size and species (or guild). It is used only in sensitivity analyses (S1 fig, S2 Table).
- Trophic Position (Tpos.csv): this dataset is the result of Delta 15 Nitrogen fractionation following Hussey 2014 and Robinson and Baum 2016. There is one TP value for each individual based on the Delta 15 Nitrogen values found in DN_individual.csv. It is used in the main analyses.
The S3_Table.csv file contains a list of reef fish species with known diet. This diet information is used in the Delta Nitrogen ~ Body mass plots to differentiate top predators, secondary consumers, and primary consumers.
The all_isotopes_DN_BM.csv contains all the Delta Nitrogen and body mass values available at the individual level. It is also used in the Delta Nitrogen ~ Body mass analyses and plots.
Variables
DN_individual.csv:
- Species: species of the individual.
- DN: Predicted Delta 15 Nitrogen value of the individual, used in the sensitivity analysis (in ‰).
- Est.Error: estimate error of the computed DN value (in ‰).
- Q2.5: lower 95% boundary for the computed DN value (in ‰).
- Q97.5: higher 95% boundary for the computed DN value (in ‰).
- Year: Sampling year of the individual.
- Transect: Sampling transect of the individual.
- Site: Sampling site of the individual.
- Abundance: retrieved abundance of the species at this transect, year, and site.
- TL: estimated total length of the individual (in cm).
- BM: computed body mass based on total length and a and b coefficients (in g).
- Archipelago: Archipelago surveyed.
- Island: Sampling the island of the individual.
- Area: area of the transect (in m).
- BM_Ab: biomass (in g/m).
- BMC: Body mass Class.
- DNC: Delta 15 Nitrogen Class.
- Diet: Known diet of the species.
Tpos.csv :
- Species: species of the individual.
- DN: Predicted Delta 15 Nitrogen value of the individual, used in the sensitivity analysis (in ‰).
- Year: Sampling year of the individual.
- Transect: Sampling transect of the individual.
- Site: Sampling site of the individual.
- Abundance: retrieved abundance of the species at this transect, year, and site.
- TL: estimated total length of the individual (in cm).
- BM: computed body mass based on total length and a and b coefficients (in g).
- Archipelago: Archipelago surveyed.
- Island: Sampling the island of the individual.
- Area: area of the transect (in m).
- BM_Ab: biomass (in g/m).
- TP: computed Trophic Position based on Delta 15 Nitrogen.
- BMC: Body mass Class.
- DNC: Trophic Position Class.
S3_Table.csv:
- family: phylogenetic family of the species.
- Species: species included in the analyses.
- p4_m to sd_tot: variables used to predict trophic guild.
- trophic_guild_predicted: predicted trophic guild based on p4_m to sd_tot variables.
- trophic_guild_predicted_text: translation of the trophic_guild_predicted value to a know guild.
all_isotopes_DN_BM.csv:
- Species: species of the individual/
- DN: individual Delta 15 Nitrogen value (in ‰).
- Archipelago: surveyed archipelago.
- BM: individual body mass value (in g).