Semester

Fall

Date of Graduation

2025

Document Type

Thesis

Degree Type

MS

College

Davis College of Agriculture, Natural Resources and Design

Department

Wildlife and Fisheries Resources

Committee Chair

Stuart Welsh

Committee Co-Chair

Brent Murry

Committee Member

Amy Welsh

Abstract

Environmental DNA (eDNA) can serve as a useful monitoring tool for cryptic and imperiled freshwater stream fishes. eDNA can fill knowledge gaps regarding species’ distribution, site abundance, and habitat usage. The last known stronghold of the Diamond Darter (Crystallaria cincotta) in the Elk River of West Virginia provides an excellent test case to examine the utility of this non-invasive method of surveying rare species. Diamond Darters are one of the most newly recognized freshwater fishes in North America and are among the most imperiled U.S. fishes, having been federally listed as endangered in 2013. The cryptic behavior and limitations of sampling methods associated with its protected status necessitate new sampling and monitoring approaches. eDNA has not yet been previously explored for the detection of the Diamond Darter. In this study, I used eDNA to investigate the historic and current range of the Diamond Darter, with the potential for amendments to the current understanding of the species’ range. To detect eDNA collected from Diamond Darter individuals via water samples, a reference assay must first be created to confidently identify Diamond Darter DNA. A unique assay was created for this investigation that allowed for eDNA detection through quantitative Polymerase Chain Reaction (qPCR), which targets a 93-base pair fragment containing a distinct Single Nucleotide Polymorphism (SNP) specific to the Diamond Darter. Encompassed by a Locked Nucleic Acid (LNA) enriched probe, the SNP distinguishes the Diamond Darter from its sister taxon, the Crystal Darter (Crystallaria asprella), as well as from other sympatric ichthyofauna. The Diamond Darter is considered extirpated from Ohio, Kentucky, and Tennessee; however, a known population continues to persist in the lower 50 river km of the Elk River in West Virginia. Extant, historical, and unknown Diamond Darter population locales were sampled for eDNA in Ohio, Kentucky, Tennessee, and West Virginia. Diamond Darter DNA was not detected in watersheds where the species is considered extirpated. Nonetheless, DNA was retrieved from seven localities within the Elk River in West Virginia, where extant Diamond Darter populations currently remain. eDNA investigations were carried out in the summer of 2024 across a total of 38 sites. A total of 137 samples were collected in four states and six bodies of water. Results were consistent with ground-truthing efforts at all positive and select non-detection localities. Follow-up nighttime spotlight investigations at positive eDNA detection sites verified the persistence of Diamond Darter occupancy in the lower Elk River. These investigations led to the discovery of a new site locality for the species ~ 24 river km above the upper extent of the critical habitat designation in the Elk River. The new occupancy detection warrants a better understanding of the Diamond Darter’s distribution. Additionally, the discovery of the new site locality supports a critical habitat range extension well upstream of the current designation for the Diamond Darter. The successes demonstrated by these investigations write a new chapter in the conservation story of the Diamond Darter. This previously untapped method of detecting and monitoring the species has proven to be an efficient, non-invasive sampling technique, offering significant benefits for improved monitoring capacity. The eDNA investigation discovered a new site locality for Elk River, thus extending the range distribution beyond the current critical habitat designation. Additionally, eDNA data provided evidence in support of the presumed extirpation status of historic distribution locations, many of which may be candidates for population repatriation efforts. This study demonstrated the successful application of eDNA for monitoring occurrence patterns of rare species, a prerequisite for improved conservation.

Download

Share

COinS