Date of Award

12-2016

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)

Department

Marine Biology

Advisor

Michael Kinnison

Second Committee Member

Rebecca Van Beneden

Third Committee Member

Joseph Zydlewski

Abstract

Invasive species cause catastrophic changes to environments they are introduced into. Early detection offers the best chance at controlling the spread and mitigating any potential damages caused by the invaders. Environmental DNA (eDNA) has emerged as a more sensitive and cost effective alternative to traditional survey approaches to detection. In this study, I designed primer-probe sets for use in quantitative PCR detection of three invasive Centrarchid species, Largemouth Bass (Micropterus salmoides), Smallmouth Bass (Micropterus dolomieu) and Black Crappie (Pomoxis nigromaculatus). I surveyed 21 water bodies in Maine during two seasons (winter and spring). I designed and validated a sampling device and protocol for through-ice water sampling for eDNA. I detected target species in all lakes where they were known to be present as well as five previously unconfirmed lakes. Through hierarchical occupancy modeling I estimated the cumulative probabilities of presence, collection and detection of eDNA at three levels of the surveys (sites, samples, qPCR replicates). Although my toolsets were effective during both seasons, spring samples contained much higher concentrations of eDNA and hierarchical occupancy models showed this season to have much higher average power to detect target species than winter. Winter is still a viable season for sampling, providing fewer contamination concerns, and with a more robust sampling protocol, would be able to provide a high level of confidence of detection. Based on my dataset, and in order to have >95% confidence of detection at each level of the survey for simple detection of presence/absence, I recommend sampling from a minimum of four sites per lake, taking three samples per site and conducting five qPCR replicates in spring and sampling from a minimum of seven sites per lake, taking five samples per site and conducting seven qPCR replicates in winter.

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