Date of Thesis

Spring 2019


As species decline globally, it is essential to determine the distribution of vulnerable species. However, rare species are often elusive and difficult to physically survey. To overcome these challenges, the analysis of environmental DNA (eDNA) has gained popularity in recent decades. By detecting DNA molecules left in the environment by organisms, we can derive information about the presence/absence of specific species as well as information about the life history of target populations because events such as breeding exhibit recognizable eDNA temporal signatures.

As a species of conservation concern, the fully-aquatic Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is well suited to survey by eDNA analysis as physical detection of these secretive salamanders in streams is time-consuming and stressful to the animals. Using the Eastern hellbender as our study species, we developed an improved protocol to increase the yield of eDNA from water samples. Our results showed that the preservation of filters at -20°C before DNA extraction and the use of bead beating during DNA extraction both significantly increase the yield of eDNA from water samples compared to preservation in ethanol and extraction without bead beating.

Secondly, we employed eDNA analysis and occupancy modelling to examine factors affecting the detection of Eastern hellbenders in the West Branch Susquehanna River. We collected water samples monthly from July to October at multiple locations across the width of the channel and analyzed the samples for eDNA from hellbenders. Our results confirmed the presence of undocumented populations of Eastern hellbenders in the West Branch Susquehanna River, contrary to current state records. We found that occupancy probability is positively influenced by site depth as well as location on the left side of the channel; we also found that eDNA detection probability increased during the breeding season when eDNA concentrations in the water are much higher due to increased activity of hellbenders.

Lastly, using eDNA analysis, we also examined breeding synchrony across populations of Eastern hellbenders in tributaries of the West Branch Susquehanna River. Through daily sampling, we were able to examine fine-scale eDNA profiles for each stream during the breeding season, observing a noticeable increase in eDNA concentration associated with breeding as well as noticeable day-to-day fluctuations in eDNA concentration. We found that the onset of breeding is asynchronous across streams and occurs 1-3 days after a marked decrease in water temperature.

Overall, in addition to refining and improving methods used during eDNA isolation, these studies contribute to the limited body of knowledge of eDNA in lotic systems and further emphasize the utility of eDNA analysis as a tool to study rare aquatic organisms.


Eastern Hellbender, Environmental DNA, Susquehanna River Basin, Cryptobranchus alleganiensis alleganiensis

Access Type

Masters Thesis (Bucknell Access Only)

Degree Type

Master of Science



First Advisor

Mizuki Takahashi

Second Advisor

Matthew McTammany

Third Advisor

Tristan Stayton