Dietary RNA: diagnostic and functional RNA offer a potential paradigm shift for molecular dietary analyses

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Just over two decades ago, DNA-based dietary analysis promised to advance the resolution, sensitivity and speed with which we could detect and identify trophic interactions. Since then, DNA-based dietary analyses have generated a paradigm shift in our understanding of trophic interactions across a wide range of natural systems. With decreasing sequencing costs and increased accessibility to sequencing technologies, adoption has broadened significantly in recent years, but advances to the practical approaches used for dietary analysis have arguably slowed. We stand now, however, at the precipice of the next advance as traditional DNA-based ecological studies increasingly apply RNA-based methods. To date, this has most commonly taken place in the context of environmental monitoring, and the application to dietary analysis is still underrepresented despite immense potential and relatively straightforward implementation. Given the increased sensitivity of RNA, the detection of prey material via RNA can mitigate many longstanding methodological pitfalls of DNA-based dietary analyses, by (i) differentiating between carrion and live prey, (ii) identifying potential false positives, and (iii) providing temporal context to detections, facilitating construction of weighted or multilayer trophic networks. Functional RNA, detected via transcriptomics, may also present an opportunity to ascribe functional context to both predator and prey, and contextualise interactions or their impact on wider trophic networks. With increasing accessibility to RNA sequencing, the application of these methods to community and network ecology may significantly advance our understanding of the drivers of trophic interactions in complex natural systems. Here, we summarise RNA-based dietary analysis methods that can be applied to dietary analysis with reference to recent literature in trophic ecology and relevant applications.

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