Date of Award

Summer 8-16-2024

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)

Department

Ecology and Environmental Sciences

Advisor

Hamish Greig

Second Committee Member

Andrew Rominger

Third Committee Member

Erin Grey

Abstract

Advancements in genetic technology and processing allows for the presence of loose genetic material in the environment to become a resource, capable of assisting habitat and wildlife management efforts by providing information about organisms in a region without having to disturb or disrupt the organisms and environment. This use of environmental DNA has gained traction across biomes, with researchers continuing to test extraction and processing of DNA from various environmental media. However, the high variability in media quality, characteristics, and taxonomic knowledge means that the tested capabilities of eDNA vary wildly depending on the application and species of interest. In this thesis, I focus on the use of eDNA metabarcoding in freshwater streams in Maine, examining the ability and existing libraries of two genetic loci to identify Maine fish and macroinvertebrate species. eDNA results are compared against a traditional specimen-based surveying method utilized by the Maine Department of Environmental Protection and the Penobscot Nation’s Department of Natural Resources, and over time to monitor the success of stream restoration initiatives. While eDNA samples successfully detected fish and invertebrate species in both datasets, no strong correlation

was found between benthic macroinvertebrate abundance counts and detected sequence variants. Furthermore, eDNA detection led to highly different community survey results than the specimen-based survey method, and limitations of available reference sequences indicate a strong need for localized references for future eDNA work. While eDNA was able to identify ASVs at a higher clarity than the specimen-based survey method, only 4 taxonomic families were shared between the survey method categorization and eDNA detection. However, eDNA was successful when applied to a broader range of taxa for presence-absence detection and community composition detection, and found that stream communities did change significantly based on installment of large wood addition projects.

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