Molecular identification and environmental DNA detection of gill lice ectoparasites associated with Brook Trout declines

Abstract Objective Gill lice Salmincola spp. are among the most widely reported parasites of freshwater salmonids and have been associated with recent declines in native Brook Trout Salvelinus fontinalis populations. Effective gill lice surveillance is vital for salmonid conservation success, but current survey approaches are often inadequate or problematic. We developed an environmental DNA (eDNA)‐based approach to detect the gill louse Salmincola edwardsii and explored the viability of this approach as a management tool for rapid, large‐scale gill lice surveillance at Fort McCoy, Wisconsin, USA. Methods Reference sequences were generated from gill lice specimens collected at Fort McCoy to confirm their identify as S. edwardsii and used to design a quantitative polymerase chain reaction (qPCR) assay that targets S. edwardsii mitochondrial cytochrome c oxidase I (COI). Assay validation included in silico and in vitro sensitivity and nontarget specificity testing, and assay performance was validated in situ by sampling eDNA at sites characterized via electrofishing. Result Molecular analysis of reference sequences confirmed S. edwardsii identity while also providing the first multi‐population assessment of genetic variation for North American Salmincola and the most taxonomically comprehensive molecular phylogeny of Lernaeopodidae to date. Salmincola edwardsii eDNA was detected at 14 of 38 sites, including 12 of 14 sites with known active infestations, with no evidence that the odds of detecting gill lice via electrofishing was greater than the odds of detections from eDNA analysis. Brook Trout presence was highly predictive of gill lice eDNA site occupancy, concordant with S. edwardsii being an obligate parasite of Salvelinus fishes. However, by expanding survey coverage via eDNA analysis, we were able to identify an isolated drainage with Brook Trout where S. edwardsii is apparently absent, confirming electrofishing observations. Conclusion These results suggest that eDNA analysis is equivalent to electrofishing for detecting gill lice in terms of performance yet offers substantial gains in survey efficiency. Further, this study demonstrates how eDNA analysis can provide valuable intel for directing management efforts, especially when used to expand survey coverage and prioritize follow‐up conventional surveys to assess host–parasite abundance, demographics, and status.