Develop a Tidewater Goby Survey Method Using Environmental DNA

US Transportation Collection2018PDFTech ReportSutter, MichaelKinziger, AndrewHumboldt State UniversityCalifornia. Dept. of Transportation. Division of Research, Innovation, and System InformationCalifornia. Dept. of Transportation. Division of Research and InnovationCaliforniaUnited StatesEndangered speciesEnvironmental monitoringFishesFresh waterSamplesTidesWater qualityCA18-272465A0580Final ReportRangewide monitoring of fish species is critical for determining status and trends in abundance and distribution; however, implementations of large-scale distribution surveys have generally been constrained by time and cost. This study uses environmental DNA (eDNA) to monitor the presence or absence of two endangered tidewater goby species, the northern tidewater goby (Eucyclogobius newberryi) and the southern tidewater goby (Eucyclogobius kristinae), across their combined geographic range that encompasses the entire California coast (1,350 km). A multi-scale occupancy model designed specifically for eDNA methods was used to account for imperfect detection and to estimate true site occupancy. A total of 209 sites were surveyed in coastal California from Del Norte to San Diego counties between May and September 2016. Among these sites, 12 were dry during the survey and assigned a status of non-detection. Among the 197 sites with water present, 430 water samples were collected, filtered, and tested for the presence/absence of northern and southern tidewater goby, using species-specific quantitative PCR (qPCR) assays. The number of water samples collected per site ranged between one and six. Northern tidewater goby were detected at 81 out of 175 sites and southern tidewater goby were detected at 4 out of 22 sites, resulting in a combined na\uefve occupancy of 0.43. In contrast, the multi-scale occupancy model estimated site occupancy at 0.55 (95% CRI 0.46\u20130.64), indicating that tidewater goby were present but not detected at 23 additional sites. Even though eDNA typically has higher detection probabilities than traditional field approaches, these findings indicate that imperfect detection needs to be accounted for in eDNA surveys. Tidewater goby were detected at seven sites where they have previously not been detected or were thought to be extirpated, including one site in San Francisco Bay.133