Best analytical practices 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 provide a comprehensive description of this necessary post-laboratory analytical workflow, 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 for the estimation of consumer trophic position and to varying sample sizes of sources and consumers. Finally, we apply the workflow to a coral reef food web to quantify fish reliance on benthic and pelagic primary production.

3. Our results indicate that estimated basal source proportions are highly sensitive to bias in the estimation of consumer trophic position, suggesting that trophic position estimation requires careful consideration of the number and nature of selected isotopic baselines. We provide an R function to quantify this bias. By contrast, the precision and uncertainty—but not the accuracy—of these proportions are influenced by the sample sizes of consumers and sources. Thus, small sample sizes can still yield valid estimations and can be included. The case study further highlights the sensitivity of estimated proportions to the selection of trophic discrimination factors (TDFs), and we suggest performing a 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 availability of data collected over the last 20 years. By providing a detailed analytical framework and identifying future directions for model development, we offer a robust analytical foundation for future isotopic studies.