Masters Theses

Orcid ID

https://orcid.org/0000-0003-3261-3517

Date of Award

12-2025

Degree Type

Thesis

Degree Name

Master of Science

Major

Life Sciences

Major Professor

Kristine Moody

Committee Members

Augustin Engman, Lisa Izzo, Paul Matson

Abstract

Freshwater biodiversity has been declining at an alarming rate, largely due to anthropogenic impacts such as impoundment caused by dams. Rigorous monitoring systems are needed for timely mitigation, yet conventional survey methods rely on capturing individuals and identifying them morphologically, which can introduce several limitations and biases. Environmental DNA (eDNA) and environmental RNA (eRNA) offer promising, non-invasive tools for studying aquatic biodiversity; however, further research is still needed to develop and standardize these methods before fully integrating them into biomonitoring programs.

This study tested eDNA and eRNA metabarcoding for detecting fish and mussel communities in the Apalachia Cutoff Reach (ACR) of the Hiwassee River, Tennessee, a 14.4-river-mile bypassed section between the Apalachia Dam and its powerhouse that is historically known to harbor endemic taxa. Water samples were collected from 19 mainstem sites and three tributaries in 2023, and molecular detections were compared to concurrent morphological surveys and historical records (1992–2016). Fish communities were analyzed using mitochondrial 12S rRNA markers from eDNA and eRNA, while mussels were assessed using cytochrome c oxidase I (COI) and 16S rRNA markers using eDNA. We also quantified the presence of the endangered eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) using qPCR on the Cytochrome b (Cytb) gene.

Despite several technical and practical challenges, both eDNA and eRNA produced consistent and ecologically meaningful results. Moreover, eDNA detected 28 fish species, eRNA detected 21, and morphological surveys recorded 16, with seven unique eDNA detections plus full overlap with eRNA. For mussels, 16S detected nine, COI detected eight species, and morphological surveys documented seven. Notably, eDNA has outperformed morphological methods in many aspects, such as detecting Venustaconcha trabalis (Endangered). Hellbenders were also detected at multiple sites consistent with historical observations, confirming the persistence of local populations.

Overall, this study shows that eDNA and eRNA metabarcoding can yield reliable results. Moreover, eDNA reflected broader species presence, while eRNA indicated more recent biological activity, offering complementary perspectives on biodiversity. These findings highlight both the promise and the challenges of molecular monitoring and provide practical insight into how eDNA and eRNA can support freshwater conservation and environmental assessment

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