Publication Date

2025

Advisor(s) - Committee Chair

Jarrett Johnson, Scott Grubbs, Natalie Mountjoy

Degree Program

Department of Biology

Degree Type

Master of Science

Abstract

Amphibian populations worldwide face severe threats, heightening the need for reliable monitoring methods. In this thesis, I explored and tested environmental DNA (eDNA) metabarcoding protocols to survey amphibian assemblages in ephemeral ponds of the the Green River Preserve in central Kentucky, USA. First, I evaluated whether the commonly used mitochondrial cytochrome c oxidase subunit I (COI) gene could effectively capture species-level variation in local amphibians for eDNA metabarcoding. Extensive primer design and testing revealed significant challenges in amplifying fragmented eDNA from water samples. In a second study, I applied a metabarcoding approach using the mitochondrial 12S ribosomal RNA (12S) gene to examine temporal variation in amphibian communities at multiple ephemeral ponds throughout a breeding season, comparing results to traditional visual encounter surveys. The metabarcoding and visual encounter survey approaches presented different data that offered a more complete picture of the species composition of our study site when examined in combination. My thesis outlines both the utility and challenges of eDNA metabarcoding for amphibian conservation, highlighting the importance of locus choice and the power of molecular methods in revealing spatiotemporal patterns of amphibian assemblages.

Disciplines

Biodiversity | Biology | Ecology and Evolutionary Biology | Genetics | Genetics and Genomics | Life Sciences | Terrestrial and Aquatic Ecology

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