Semester

Spring

Date of Graduation

2026

Document Type

Thesis

Degree Type

MS

College

Davis College of Agriculture, Natural Resources and Design

Department

Wildlife and Fisheries Resources

Committee Chair

Amy Welsh

Committee Co-Chair

Dawn Washington

Committee Member

Adrianne Brand

Committee Member

Eric Hileman

Abstract

Habitat fragmentation has the potential to isolate localized populations, particularly those which are understood to have limited dispersal capabilities. This isolation can reduce genetic diversity through the effects of inbreeding depression, and small populations are more susceptible to the impacts of genetic drift. In this study, I aim to understand the level of genetic connectivity between known occupied patches of Cheat Mountain salamanders (Plethodon nettingi; CMS) on managed public land. CMS are a federally threatened, high-elevation, West Virginia endemic species associated with red spruce (Picea rubens) forests. I used double-digest restriction site associated DNA (ddRAD) sequencing methods to sample 139 individuals across five patches, generating two datasets: a selective set with 602 single nucleotide polymorphisms (SNPs) and a neutral set with 4,803 SNPs. Despite anthropogenic barriers due to historic logging practices, I found measures of Nei’s genetic distance (D), pairwise fixation indices (FST), and inbreeding coefficients (FIS) to be low. Additionally, I found no evidence of isolation-by-distance (Mantel r = 0.139, p = 0.317). These results suggest that the patches appear to be genetically connected with admixture occurring between two populations. I also tested Flinders Technology Associates (FTA) cards, which are used widely to collect and store genetic samples, as they provide a dry, room temperature alternative to freezing and DNA can be retrieved after long-term storage. I collected tissue and skin swabs from 42 individuals to compare samples on a one-to-one basis. The average number of retained reads for tissue samples was 2,008,664 and 2,791 for FTA cards. Genotyping produced 549,704 loci for tissue and 7,509 loci for FTA samples. Parameterized calls for SNPs retained 69,141 for tissue and 10 for FTA. Based on these results, I conclude the tested protocols were not compatible and future projects should investigate how to increase the amount of genetic material available on the FTA cards or subsamples to facilitate downstream analyses.

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