Establishing the signal above the noise: Accounting for an environmental background in the detection and quantification of salmonid environmental DNA
| dc.contributor.author | Hocking, Morgan D. | |
| dc.contributor.author | MacAdams, Jeffrey C. | |
| dc.contributor.author | Allison, Michael J. | |
| dc.contributor.author | Bergman, Lauren C. | |
| dc.contributor.author | Sneiderman, Robert | |
| dc.contributor.author | Koop, Ben F. | |
| dc.contributor.author | Starzomski, Brian M. | |
| dc.contributor.author | Lesperance, Mary L. | |
| dc.contributor.author | Helbing, Caren C. | |
| dc.date.accessioned | 2022-11-07T19:49:50Z | |
| dc.date.available | 2022-11-07T19:49:50Z | |
| dc.date.copyright | 2022 | en_US |
| dc.date.issued | 2022 | |
| dc.description.abstract | A current challenge for environmental DNA (eDNA) applications is how to account for an environmental (or false-positive) background in surveys. We performed two controlled experiments in the Goldstream Hatchery in British Columbia using a validated coho salmon (Oncorhynchus kisutch) eDNA assay (eONKI4). In the density experiment at high copy number, eDNA in 2 L water samples was measured from four 10 kL tanks containing 1 to 65 juvenile coho salmon. At these densities, we obtained a strong positive 1:1 relationship between predicted copy number/L and coho salmon biomass (g/L). The dilution experiment simulated a situation where fish leave a pool environment, and water from upstream continues to flow through at rates of 141–159 L/min. Here, three coho salmon were placed in four 10 kL tanks, removed after nine days, and the amount of remaining eDNA was measured at times coinciding with dilutions of 20, 40, 80, 160, and 1000 kL. The dilution experiment demonstrates a novel method using Binomial–Poisson distributions to detect target species eDNA at low copy number in the presence of an environmental background. This includes determination of the limit of blank with background (LOB-B) with a controlled false positive rate, and limit of detection with background (LOD-B) with a controlled false negative rate, which provides a statistically robust “Detect” or “No Detect” assessment for eDNA surveys. | en_US |
| dc.description.reviewstatus | Reviewed | en_US |
| dc.description.scholarlevel | Faculty | en_US |
| dc.description.sponsorship | Initial funding for data collection was provided by the Hakai Institute to support the graduate student project of JCM supervised by BMS and MDH in the School of Environmental Studies at the University of Victoria. The Ian McTaggart Cowan Professorship and an NSERC Discovery Grant (RGPIN 2017-04476) to BMS further supported this research during the data collection. Further funding was provided by a Mitacs Accelerate grant (IT09814) for JCM to BMS and CCH in partnership with Ecofish Research Ltd., and a Natural Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development Grant (CRDPJ 523633-18) to CCH and MLL, including student support for RS, in partnership with Ecofish Research Ltd. The project was also supported by Research & Development (R&D) funding to MDH and JCM by Ecofish Research Ltd. | en_US |
| dc.identifier.citation | Hocking, M. D., MacAdams, J. C., Allison, M. J., Bergman, L. C., Sneiderman, R., Koop, B. F., . . . Helbing, C. C. (2022). “Establishing the signal above the noise: Accounting for an environmental background in the detection and quantification of salmonid environmental DNA.” Fishes, 7(5), 266. https://doi.org/10.3390/fishes7050266 | en_US |
| dc.identifier.uri | https://doi.org/10.3390/fishes7050266 | |
| dc.identifier.uri | http://hdl.handle.net/1828/14407 | |
| dc.language.iso | en | en_US |
| dc.publisher | Fishes | en_US |
| dc.subject | eDNA methods development | en_US |
| dc.subject | false-positive error | en_US |
| dc.subject | false-negative error | en_US |
| dc.subject | fisheries monitoring | en_US |
| dc.subject | limit of blank with background | en_US |
| dc.subject | limit of detection with background | en_US |
| dc.subject | low copy number | en_US |
| dc.subject | salmonids | en_US |
| dc.subject | qPCR assays | en_US |
| dc.title | Establishing the signal above the noise: Accounting for an environmental background in the detection and quantification of salmonid environmental DNA | en_US |
| dc.type | Article | en_US |