Date of Award

Summer 8-20-2021

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)


Ecology and Environmental Sciences


Michael Kinnison

Second Committee Member

Phillip deMaynadier

Third Committee Member

Joseph Zydlewski


Whether considering an expanding non-native species or a priority native species with a dwindling local population, the monitoring of low-abundance, sporadically distributed, or otherwise elusive populations, can prove difficult. In separate studies, we tested the viability of environmental DNA (eDNA) for monitoring a species in both of the above circumstances, the common mudpuppy (Necturus maculosus), a spreading non-native species, and rainbow smelt (Osmerus mordax), a declining species of concern. Mudpuppy are fully aquatic salamanders that were introduced to the Belgrade region of central Maine in 1939 and again in 1940. Though they had been present for nearly 80 years when this study began, their ecological impacts and secondary spread have not been well documented. Following a year of trapping through the winter ice, eDNA methods were added concurrently with traditional trapping techniques to demine if detection could be improved in order to better document secondary spread and estimate abundance. Overall, eDNA was helpful in this effort as mudpuppy were detected in all but one waterbody where they were trapped and in two where they were not. Occupancy models were used to estimate survey power and sampling efforts for 95% probability of detection based on our data. Trapping and eDNA showed comparable power at the level of lake regions and number of sampling holes. However, when looking at the level of technical replicates, trap data required 6.4 replicates (trapping events) while eDNA required 10.9 (qPCR replicates). However, the amount of work and expense to obtain qPCR replicates is likely less than to implement additional days of trapping. Trap and eDNA sampling depth data were also used to gain preliminary insight on environmental preferences. Kologorov Smirnoff tests comparing overall depth distribution and individual mudpuppy caught at a given trap site did not reveal an observable trend in depth preferences. T-tests revealed a modest preference for 4-8m depths, but this was likely due to depths available in study sites as opposed to true biological preference. Overall, the combined results of trapping and eDNA sampling both suggest that the mudpuppy invasion has been relatively gradual, and provided baseline occupancy information for potential future assessments of range expansion. In the second study of this thesis, we assessed eDNA as a means to monitor anadromous rainbow smelt (Osmerus mordax), a species of special conservation concern in Maine. As anadromous fish, rainbow smelt migrate up streams and rivers to spawn during the early spring period when typical nighttime visual surveys can be difficult or even dangerous. As such, the current use of many coastal streams for spawning is poorly known. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat. However, the lotic environments and behavior of smelt present potential challenges for eDNA. Rainbow smelt often enter smaller streams at night and depart by morning, such that fish eDNA might be flushed out of the system relatively quickly. By combining daytime eDNA sampling with fyke netting, we confirmed that smelt eDNA could be detected up to weeks following peak spawning events. Indeed, there was some evidence that concentration of eDNA (copies/L) rose over the approximately 8-13 days following spawning events, suggesting developing and hatching smelt larvae might be the primary source of residual eDNA. Adding to this study, we conducted eDNA surveys in four streams of varying smelt abundance and estimated sampling effort for 95% detection probability using occupancy modelling. Ultimately, results suggested that at the stream with least detections, sampling effort involving collection of three water samples, collected on three days, and analyzed with six qPCR replicates would provide ≥ 95% detection probability. Comparing those recommendations to the sampling design used in this study, the number of qPCR replicates used was the only sampling value below our generated recommendations. These results demonstrate that eDNA methods can be effective for monitoring smelt in lotic systems during their breeding period, particularly with a modest increase in sample processing effort to increase detection probabilities.