Date of Award

8-2025

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Doctor of Philosophy (PhD)

Department

Marine Biology

First Committee Advisor

Kristina Cammen

Second Committee Member

Michael Kinnison

Third Committee Member

Damian Brady

Additional Committee Members

Erin Grey

Graham Sherwood

Abstract

Coastal ecological communities face a variety of anthropogenic impacts including exploitation, habitat alteration, and climate change. Even when such changes are intended to be ecologically beneficial (e.g., habitat restoration, changes in policy or resource management), they can have wide-reaching impacts. Ecological monitoring is an important part of assessing the effectiveness of such efforts, understanding ecological processes, and anticipating future changes. However, the tools available to accomplish this task are highly varied, and employing these established techniques can be resource- and time-intensive, especially when monitoring across broad taxonomic groups or spatiotemporal scales. Environmental DNA offers a less invasive, potentially more efficient method of gathering data on aquatic communities, but is less developed than many traditional assessment tools. This dissertation contributes to the growing applicability of these methods by evaluating their effectiveness at community and population assessment on broad, local, and intraspecific scales. I first use eDNA methods to assess fish community composition and phenology in the Penobscot River Estuary, where recent restoration efforts have led to the recovery of ecologically important fish populations. By comparing eDNA data to hydroacoustics and trap counts of migrating fish, I found that these eDNA data aligned well to complimentary data streams and could provide new perspectives on community composition and phenology. I then applied these tools on a larger scale, using them to assess taxonomic and environmental drivers of community variation across estuaries and bays along the coast of Maine. I detected distinct fish communities across habitat types and sites, often driven by the relative proportion of diadromous fish and Atlantic herring, as well as spatial and environmental variables such as longitude and salinity. By using this data to compare patterns of co-detection between striped bass and multiple prey species, I also provide evidence of the potentially growing role of river herring as prey for these predators. Finally, I focus on one species, the gray seal, and use eDNA tools to identify genetic variants from the water surrounding large haulout sites on Cape Cod, Massachusetts. This works demonstrates that eDNA sampling can capture population-level allele frequencies and may be sensitive enough to detect new haplotypes, although a higher amount of sampling effort may be needed to conduct a full census of such large groups of animals. Overall, this work demonstrates the suitability and efficiency of these tools and highlights important considerations for future use.

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