An analytical workflow for estimating consumer reliance on basal food sources using bulk stable isotopes

Mattia Ghilardi , Renato A. Morais, Simon J. Brandl, Jordan M. Casey, Alexandre Mercière, Fabien Morat, Nina M. D. Schiettekatte, Mohsen Kayal, Yves Letourneur, Valeriano Parravicini

1. Bulk stable isotopes have been utilised by ecologists for decades to trace the assimilation of basal food sources across trophic positions. However, there is a lack of guidance on the post-laboratory analytical workflow, leading to inconsistencies in how isotopic data are processed and interpreted.
  
2. We consolidate existing methods into a comprehensive description of this necessary post-laboratory analytical workflow for consumers several trophic steps above basal sources, including the mathematical rationale underlying the estimation of consumer reliance on basal sources. Using simulated data, we test the sensitivity of estimated basal source proportions to the number of isotopic baselines used to estimate consumer trophic position, the sample sizes of sources and consumers, and uncertainty in trophic discrimination factors (TDFs). Finally, we apply the workflow to a coral reef food web to quantify fish reliance on benthic and pelagic primary production.
  
3. Estimated basal source proportions were highly sensitive to bias in consumer trophic position, which also reduced the coverage of their credible intervals, as these intervals are conditional on the estimated trophic position. Trophic position estimation therefore requires careful consideration of the number and nature of selected isotopic baselines, and we provide an R function to quantify this bias. The precision and uncertainty, but not the accuracy, of source proportions were influenced by the sample sizes of consumers and sources, so small sample sizes can still be included at the cost of lower precision. Accounting for TDF uncertainty in the mixing model had limited effects, whereas a misspecified mean TDF biased trophic position and reduced credible interval coverage. The case study further highlights the sensitivity of estimated proportions to the choice of TDFs, and we recommend sensitivity analysis with alternative TDFs.
  
4. While compound-specific stable isotope analysis is gaining prominence, bulk stable isotope analysis remains a cornerstone for field ecologists due to its high throughput, cost-effectiveness and the availability of data collected over the last 20 years. By detailing the analytical framework and identifying future directions for model development, we provide a foundation for future isotopic studies.