Environmental DNA applications: Developing quantitative PCR assays for 20 New Brunswick freshwater fishes

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University of New Brunswick


Canadian freshwater fishes are a diverse group of vertebrates, some of which are undergoing significant population declines. To detect and monitor freshwater fishes, the use of environmental DNA (eDNA) has been employed widely over the past fifteen years. Quantitative polymerase chain reaction (qPCR) assays are the molecular tool used to detect eDNA by binding to DNA segments unique to each species. There is a lack of specific and sensitive Cytochrome B qPCR assays for Canadian freshwater fishes. I developed fourteen novel assays and modified six pre-existing assays for twenty New Brunswick freshwater fishes. All twenty assays successfully detected DNA of their corresponding target species, three of which were species-specific against off-target species tested. Five assays were tested on eDNA samples from two rivers at Fundy National Park and successfully detected four target species. The eDNA assays from this study can be used as molecular detection tools across the broad geographic regions where these fishes are found.