Data and code from: Energy channel coupling by mid-trophic level fish challenges the landscape theory for food web architecture in a large tropical lake ecosystem
Data files
Jul 29, 2026 version files 184.53 KB
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AB_source.csv
143 B
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BF_source.csv
143 B
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HF_source.csv
143 B
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LN_source.csv
143 B
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Muehl_et_al_Energy_Channel_Coupling.R
117.23 KB
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ON_source.csv
143 B
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README.md
9.18 KB
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tef_AB.csv
93 B
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tef_BF.csv
89 B
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tef_HF.csv
89 B
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tef_LN.csv
93 B
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tef_ON.csv
89 B
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Turkana_IsotopeData_Master.csv
56.95 KB
Abstract
Landscape theory for food web architecture (LTFWA) posits that the stability of food webs is supported by the coupling of fast pelagic and slow littoral energy channels mediated by large mobile consumers. Empirical tests of the LTFWA are limited, and support for the LTFWA varies among and within aquatic ecosystems. While the LTFWA is thought to be supported in large lake ecosystems, empirical studies have focused on temperate environments with little emphasis on large tropical lake ecosystems. Lake Turkana, a climatically sensitive East African Great Lake, is a highly resilient desert lake and an ideal model for examining how consumer fish species may mediate the coupling of fast and slow energy channels within food webs in a large tropical lake ecosystem. To empirically test the LTFWA, we explored the ecological niche characteristics of five important Lake Turkana fish species including Alestes baremoze, Brachyalestes ferox, Hydrocynus forskahlii, Lates niloticus, and Oreochromis niloticus across ontogeny and used a Bayesian isotope mixing model approach to identify which species play important roles in coupling the fast pelagic and slow littoral energy channels. We reveal that mid-trophic level fish species like A. baremoze, B. ferox, and O. niloticus play important roles in coupling energy channels in Lake Turkana, subverting expectations that upper trophic level consumers H. forskahlii and L. niloticus would couple energy channels the most. We demonstrate that the energy coupling patterns proposed by the LTFWA are not ubiquitously supported across all large lake ecosystems, and small-bodied mid-trophic level fish species are vital for coupling energy channels in Lake Turkana. Thus, fisheries management in Lake Turkana should aim to sustain populations of mid-trophic level species that couple pelagic and littoral energy channels via a multispecies approach that considers interspecific trophic interactions between targeted fish species.
All isotopic data, metadata, and R code related to the manuscript entitled: "Energy channel coupling by mid-trophic level fish challenges the landscape theory for food web architecture in a large tropical lake ecosystem" by M.F. Muehl, J.A. Olin, J.L. Keyombe, J.Y. Aller, and R.M. Cerrato are provided here.
Dataset DOI: 10.5061/dryad.bnzs7h4r1
Description of the data and file structure
Files and variables
File: Muehl_et_al_Energy_Channel_Coupling.R
Description: Annotated code for all analyses.
File: tef_LN.csv
Description: Trophic enrichment factor values for L. niloticus formatted for mixing model analyses with MixSIAR
Variables
- Means: Pelagic or Littoral trophic enrichment factor description
- Meand13C: Mean δ13C values for littoral and pelagic trophic enrichment factors
- SDd13C: Standard deviations for δ13C values for littoral and pelagic trophic enrichment factors
- Meand15N: Mean δ15N values for littoral and pelagic trophic enrichment factors
- SDd15N: Standard deviations for δ15N values for littoral and pelagic trophic enrichment factors
File: tef_ON.csv
Description: Trophic enrichment factor values for O. niloticus formatted for mixing model analyses with MixSIAR
Variables
- Means: Pelagic or Littoral trophic enrichment factor description
- Meand13C: Mean δ13C values for littoral and pelagic trophic enrichment factors
- SDd13C: Standard deviations for δ13C values for littoral and pelagic trophic enrichment factors
- Meand15N: Mean δ15N values for littoral and pelagic trophic enrichment factors
- SDd15N: Standard deviations for δ15N values for littoral and pelagic trophic enrichment factors
File: tef_HF.csv
Description: Trophic enrichment factor values for H. forskahlii formatted for mixing model analyses with MixSIAR
Variables
- Means: Pelagic or Littoral trophic enrichment factor description
- Meand13C: Mean δ13C values for littoral and pelagic trophic enrichment factors
- SDd13C: Standard deviations for δ13C values for littoral and pelagic trophic enrichment factors
- Meand15N: Mean δ15N values for littoral and pelagic trophic enrichment factors
- SDd15N: Standard deviations for δ15N values for littoral and pelagic trophic enrichment factors
File: tef_AB.csv
Description: Trophic enrichment factor values for A. baremoze formatted for mixing model analyses with MixSIAR
Variables
- Means: Pelagic or Littoral trophic enrichment factor description
- Meand13C: Mean δ13C values for littoral and pelagic trophic enrichment factors
- SDd13C: Standard deviations for δ13C values for littoral and pelagic trophic enrichment factors
- Meand15N: Mean δ15N values for littoral and pelagic trophic enrichment factors
- SDd15N: Standard deviations for δ15N values for littoral and pelagic trophic enrichment factors
File: tef_BF.csv
Description: Trophic enrichment factor values for B. ferox formatted for mixing model analyses with MixSIAR
Variables
- Means: Pelagic or Littoral trophic enrichment factor description
- Meand13C: Mean δ13C values for littoral and pelagic trophic enrichment factors
- SDd13C: Standard deviations for δ13C values for littoral and pelagic trophic enrichment factors
- Meand15N: Mean δ15N values for littoral and pelagic trophic enrichment factors
- SDd15N: Standard deviations for δ15N values for littoral and pelagic trophic enrichment factors
File: AB_source.csv
Description: Source isotope values for A. baremoze formatted for mixing model analyses with MixSIAR
Variables
- Column header intentionally blank to fulfill the necessary formatting for mixing model analysis with MixSIAR
- Meand13C: Mean δ13C values for littoral and pelagic sources
- SDd13C: Standard deviations for δ13C values for littoral and pelagic sources
- Meand15N: Mean δ15N values for littoral and pelagic sources
- SDd15N: Standard deviations for δ15N values for littoral and pelagic sources
- n: Sample size for littoral and pelagic sources
File: BF_source.csv
Description: Source isotope values for B. ferox formatted for mixing model analyses with MixSIAR
Variables
- Column header intentionally blank to fulfill the necessary formatting for mixing model analysis with MixSIAR
- Meand13C: Mean δ13C values for littoral and pelagic sources
- SDd13C: Standard deviations for δ13C values for littoral and pelagic sources
- Meand15N: Mean δ15N values for littoral and pelagic sources
- SDd15N: Standard deviations for δ15N values for littoral and pelagic sources
- n: Sample size for littoral and pelagic sources
File: HF_source.csv
Description: Source isotope values for H. forskahlii formatted for mixing model analyses with MixSIAR
Variables
- Column header intentionally blank to fulfill the necessary formatting for mixing model analysis with MixSIAR
- Meand13C: Mean δ13C values for littoral and pelagic sources
- SDd13C: Standard deviations for δ13C values for littoral and pelagic sources
- Meand15N: Mean δ15N values for littoral and pelagic sources
- SDd15N: Standard deviations for δ15N values for littoral and pelagic sources
- n: Sample size for littoral and pelagic sources
File: LN_source.csv
Description: Source isotope values for L. niloticus formatted for mixing model analyses with MixSIAR
Variables
- Column header intentionally blank to fulfill the necessary formatting for mixing model analysis with MixSIAR
- Meand13C: Mean δ13C values for littoral and pelagic sources
- SDd13C: Standard deviations for δ13C values for littoral and pelagic sources
- Meand15N: Mean δ15N values for littoral and pelagic sources
- SDd15N: Standard deviations for δ15N values for littoral and pelagic sources
- n: Sample size for littoral and pelagic sources
File: ON_source.csv
Description: Source isotope values for O. niloticus formatted for mixing model analyses with MixSIAR
Variables
- Column header intentionally blank to fulfill the necessary formatting for mixing model analysis with MixSIAR
- Meand13C: Mean δ13C values for littoral and pelagic sources
- SDd13C: Standard deviations for δ13C values for littoral and pelagic sources
- Meand15N: Mean δ15N values for littoral and pelagic sources
- SDd15N: Standard deviations for δ15N values for littoral and pelagic sources
- n: Sample size for littoral and pelagic sources
File: Turkana_IsotopeData_Master.csv
Description: Master data file containing isotope values and all associated metadata for all fish samples collected. "NULL" was used to fill cells for which data was not collected (e.g., fork lengths for species that do not have forked caudal fins).
Variables
- d13C: Muscle tissue δ13C values
- d15N: Muscle tissue δ15N values
- percent_C: Percent carbon for each sample
- percent_N: Percent nitrogen for each sample
- CN: Carbon to nitrogen ratio for each sample
- Field_ID: Field identification number for each sample
- Catch Date: Catch date for each sample
- Year: Catch year for each sample
- Species: Fish species (Genus and species)
- Site: Littoral or pelagic site description
- Preferred_Length: Length (cm) used for mixing model analysis. Fork length is preferred for species where measuring a fork length is possible, and total length is preferred for species where measuring a fork length is not possible. This is included as a column to streamline the code for mixing model analyses with length as a covariate.
- Total_Length: Length (cm) from tip of snout to the end of the caudal fin
- Fork_Length: Length (cm) from tip of snout to the inside of the caudal fin fork. This is only collected for fish species with forked caudal fins.
- Maturity: Maturity status determined from macroscopic gonad staging (immature or mature).
- Sex: Sex determined from macroscopic gonad staging (male, female, or immature).
- Reproductive_Stage: Reproductive stage determined from macroscopic gonad staging (1-5)
Code/software
Excel or R can be used to view the data .csv files. All code is included as a .R file, and all code has been annotated in the R script with a Table of Contents that explains all steps of the analyses. All R script annotations are included in a point-by-point format to explain the purpose of each line of code. All R packages necessary for analyses are detailed in "PART 1" with annotated descriptions of their purposes alongside the code to load each package. The Table of Contents, also detailed within the R script is as follows:
TABLE OF CONTENTS
PART 1: Loading packages and creating functions for mixing model use in PART 8
PART 2: Lipid correction for d13C data
PART 3: Summary statistics and testing for normality and homogeneity of variance
PART 4: Univariate pairwise comparisons
PART 5: Multivariate pairwise comparisons
PART 6: Isotopic niche analyses with SIBER
PART 7: Isotopic niche overlap analyses with nicheROVER
PART 8: Bayesian isotopic mixing models for each species with covariates
White muscle tissue was collected from five fish species, Alestes baremoze (n=98), Brachyalestes ferox (n=60), Hydrocynus forskahlii (n=124), Lates niloticus (n=88), and Oreochromis niloticus (n=119), captured from five littoral and five pelagic sampling sites from the western marsh of Ferguson's Gulf to Central Island (Figure 1). Fish were captured during fisheries independent surveys in January 2022, 2023, and 2024 using surface-set, unbaited scientific monofilament gillnets (68.6m long, 3.1m deep). Each gillnet contained 15 mesh panels (each 4.6m long) with stretched mesh sizes of 2.5, 3.8, 5.1, 6.4, 7.6, 8.9, 10.1, 12.7, 14.0, 15.2, 16.5, 17.8, 20.3, and 21.6 cm. Survey sampling sites were randomly selected within the bounds of the established Ferguson's Gulf littoral fishery and the bounds of the currently expanding pelagic fishery. Two gillnets were deployed at each sampling site between 0600 and 1000h and were retrieved after a soak time of 6h. Upon capture, fish were measured for total length (cm) and fork length (cm, when applicable) and weighed (kg). Sex, maturity status, and reproductive stage were determined for each fish via dissection during fieldwork and macroscopic gonad staging methods developed by Hopson (1982) and described in Table S1. Due to logistical constraints, sex and maturity data were not collected for L. niloticus.
