What’s in a name? Bioinformatics and the challenge of using eDNA metabarcoding to report non-indigenous species detections

Paula Pappalardo, Katrina M. Paggenkopp-Lohan, Sarah A. Brown, John Darling 

Environmental DNA (eDNA) metabarcoding is increasingly employed for surveillance of non-indigenous species (NIS), offering the promise of simultaneous multi-taxon de-tection, scalability, and the capacity for early detection before populations become es-tablished. The sensitivity of metabarcoding that makes it attractive for NIS surveil-lance also creates a meaningful risk of erroneous detections and this risk is com-pounded by the extraordinary nature of NIS surveillance itself: The target signal, by definition, is not expected to be present. Here, we describe three validation criteria that practitioners should consider when evaluating their confidence in putative NIS detec-tions from metabarcoding datasets. These are: (1) the strength of the detection signal; (2) the ecological plausibility of the detection; and (3) the confidence in the taxonomic assignment. We argue that the metabarcoding community working on NIS detection would benefit from a more deliberate and transparent approach to reporting—one that explicitly acknowledges the uncertainty surrounding any given detection and contex-tualizes it within this structured evaluation framework. We do not provide quantita-tive thresholds for confirming NIS detections or specify any explicit implementation of the proposed framework, as such determinations will depend on the ecological and management context and are appropriately made in dialogue between the scientists reporting detections and the managers who must act on them. That said, we believe that the considerations outlined here should be seriously considered by both data pro-viders and end-users who intend to utilize eDNA metabarcoding to report NIS, partic-ularly when such reporting might trigger management action.