Detection of brook trout in spatiotemporally separate locations using validated eDNA technology

Abstract

Brook trout are a species of conservation concern in Southwestern Ontario, Canada, and effective monitoring of their populations is crucial for making informed management decisions. Electrofishing is a traditional, yet invasive, method that allows for fish abundance estimation. Environmental DNA (eDNA) is an emerging molecular tool that presents a non-invasive alternative to electrofishing. This study was a collaborative effort between researchers in academia, industry, and an NGO, with the following objectives: 1) compare eDNA detections with electrofishing when monitoring brook trout populations in a site of known occupancy, 2) compare existing eDNA collection methods, and 3) extend eDNA surveys to regions of unknown occupancy that could be of conservation concern (Hanlon Creek and Twelve Mile Creek, Ontario). First, eDNA sampling methods were validated with standard electrofishing. Water samples were filtered in tandem at each site using two commercially available eDNA samplers. The results suggest a significant difference in total eDNA capture and incidence of PCR inhibitors between the two autosamplers. Brook trout eDNA was detected at all locations in Hanlon Creek in September and November, as well as 5/6 sampling locations in Twelve Mile Creek. Brook trout signal in Hanlon Creek was stronger in November compared to September 2019, suggesting possible spawning activity. Brook trout eDNA was also detected in Twelve Mile Creek where brook trout were previously unreported. This study provides a technical validation for the use of eDNA in brook trout monitoring and illustrates the opportunity to use eDNA surveys in regulated settings to complement and improve conventional biomonitoring methods for the management of elusive species.

Commercial production of Florida pompano (Trachinotus carolinus) larvae at low salinity induces variable changes in whole-larvae microbial diversity, gene expression, and gill histopathology

“…These filters were kept at room temperature until time of extraction. Smith-Root conducted a study showing that DNA did not degrade within 6 months at room temperature (Thomas et al, 2019) and these filters have also been used in other studies (Loeza-Quintana et al, 2020;Skinner et al, 2020;Banks et al, 2021;Nolan et al, 2022). These self-preserving eDNA filters are made of hydrophilic plastic which absorbs any remaining moisture into the package and preserves the DNA and prokaryotes via desiccation which has been shown as an effective preservation technique in other studies (Garcıá, 2011;Manzanera, 2021).…”

Optimization of environmental DNA-based methods: A case study for detecting brook trout (Salvelinus fontinalis).

“…It is well-established that eDNA-based detection sensitivity is superior to conventional methods for fishes, which are the dominant taxa of interest in the eDNA literature (Hänfling & Lawson-Handley, 2021). Several studies have demonstrated the ability of eDNA-based methods to corroborate conventional survey data and further detect species not captured by conventional methods (Li et al, 2019;McDevitt et al, 2019;Nolan et al, 2023). Beyond simple presence/absence determination, eDNA has been used for semi-quantitative abundance assessment by establishing a correlation between population biomass and eDNA quantity or site occupancy across spatial replicates (Bourque et al, 2023;Evans et al, 2016;Li et al, 2019).…”

Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context

“…Once the reliability and repeatability of these technics are assessed, they can be embedded into management policies as it happened in the UK (reported by Handley et al, 2022). Despite the bias derived the variability in the spatio-temporal distribution of eDNA in the marine environment (reviewed by Rourke et al, 2021), its successful application in the detection of the brook trout (Salvelinus fontinalis) in spatially distinct sampling locations (i.e., small spatial scales: largest straight distance between two sites was 1.3 and 6.2 km) (Nolan et al, 2022) could potentially make it appropriate to be implemented in the management of SSFs (i. e., monitoring of sites at regional scales). Advancements in this field have been recently applied to abalone conservation: for example, to monitoring abundances of the northern abalone, H. kamtschtkana and detection of local genetic diversity of H. iris in New Zealand (Adam et al, 2022).…”