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Abstract Assessments of ecosystem functioning are a fundamental ecological challenge and an essential foundation for ecosystem‐based management. Species trophic position (TP) is essential to characterize food web architecture. However, despite the intuitive nature of the concept, empirically estimating TP is a challenging task due to the complexity of trophic interaction networks. Various methods are proposed to assess TPs, including using different sources of organic matter at the base of the food web (the ‘baseline’). However, it is often not clear which methodological approach and which baseline choices are the most reliable. Using an ecosystem‐wide assessment of a tropical reef (Marquesas Islands, with available data for 70 coral reef invertebrate and fish species), we tested whether different commonly used TP estimation methods yield similar results and, if not, whether it is possible to identify the most reliable method. We found significant differences in TP estimates of up to 1.7 TPs for the same species, depending on the method and the baseline used. When using bulk stable isotope data, the choice of the baseline significantly impacted TP values. Indeed, while nitrogen stable isotope (δ15N) values of macroalgae led to consistent TP estimates, those using phytoplankton generated unrealistically low TP estimates. The use of a conventional enrichment factor (i.e. 3.4‰) or a ‘variable’ enrichment factor (i.e. according to feeding guilds) also produced clear discrepancies between TP estimates. TPs obtained with δ15N values of source amino acids (compound‐specific isotope analysis) were close to those assessed with macroalgae. An opposite seasonal pattern was found, with significantly lower TPs in winter than in summer for most species, with particularly pronounced differences for lower TP species. We use the observed differences to discuss possible drivers of the diverging TP estimates and the potential ecological implications.

Abstract The dugong (Dugong dugon), a large marine mammal herbivore of the Indo-Pacific, is vulnerable to extinction at a global scale due to a combination of human-related threats including habitat degradation. The species forages on seagrass habitats (marine phanerogams) and plays a key role in the functioning and sensitivity of these declining coastal ecosystems. The trophic behaviour and plasticity of dugong populations in response to extrinsic and intrinsic factors are therefore crucial features to both dugong and seagrass conservation. Yet, this knowledge remains limited to few visual observations and analyses of mouth, stomach or faecal contents of stranded individuals. We take advantage of a long-term monitoring of stranded individuals from the endangered New Caledonian population to depict features of dugongs’ trophic ecology from Carbon and Nitrogen stable isotopes. A total of 59 dugong skin samples were used to portrait the stable isotope niche of dugongs according to their sex and maturity. In light of previous work conducted in New Caledonia, a subset of these samples was used to model the trophic mix of dugong males and females. Our stable isotope mixing models used C and N isotope values of 10 taxa bbelonging to five divisions of metazoans, plants, and chromists. Our results represent the first estimate of the species dietary niche in the isotopic space. They suggest that the diet of dugong calves overlaps more with that of adult females (δ13C: − 6.38 ± 1.13 ‰; δ15N: 2.49 ± 1.10 ‰) than males (δ13C: − 5.92 ± 1.10 ‰; δ15N: 3.69 ± 1.28 ‰). Further, we highlight differences in the expected trophic mix of dugong adult males and females. From these, we formulate a sex-specific foraging behaviour hypothesis in dugongs, whereby lactating females could forage over smaller spatial ranges but more diverse food sources thanmales. The study emphasizes the importance of long-term stranding monitoring programs to study the ecology of marine mammals.. Finally, it depicts an ecological feature that may contribute to the sensitivity of vulnerable dugongs to ongoing changes on tropical coastal ecosystems.