Author ORCID Identifier

https://orcid.org/0000-0002-0478-950X

Semester

Summer

Date of Graduation

2026

Document Type

Dissertation

Degree Type

PhD

College

Davis College of Agriculture, Natural Resources and Design

Department

Wildlife and Fisheries Resources

Committee Chair

Amy Welsh

Committee Co-Chair

Christopher Rota

Committee Member

Sheldon Owen

Committee Member

Mack Frantz

Abstract

Snowshoe hares (Lepus americanus) occupy a large range across the United States and Canada. While snowshoe hare populations are generally considered stable in the interior of their range, populations along range edges are experiencing declines, possibly driven by climate-related factors such as seasonal coat color mismatch. West Virginia represents one of the southernmost extents of the species’ range, yet little is known about the population genetic status or population sizes of snowshoe hares in the state. Appalachian cottontails (Sylvilagus obscurus) are another lagomorph species found in West Virginia. This species experienced a historical decline and currently exist in small, fragmented populations across their range. Although Appalachian cottontails are considered a vulnerable species (S3 state conservation status rank) in West Virginia, little is known about their population genetic status. Vulnerable species often exist at small population sizes and are prone to issues that could threaten their persistence. In addition to the aforementioned concerns for both species, rabbit hemorrhagic disease virus 2 (RHDV2) is a highly contagious viral disease that is usually fatal for rabbit and hare species and is especially concerning for the persistence of vulnerable species.

As such, the goals of this dissertation were to (1) assess population genetic structure, measure genetic diversity, and assess the influence of landscape on genetic differentiation for both Appalachian cottontails and snowshoe hares in the state of West Virginia, (2) estimate population density of snowshoe hares at multiple sites in the state and relate density to environmental features, (3) use a conditional autoregressive model (CAR) to better understand environmental influences on RHDV2 cases in wild lagomorphs across the US, (4) use spatial parameters from the CAR model to visually and quantitively assess the spread of RHDV2 in West Virginia, and lastly (5) to develop a guide for using metabarcoding to characterize gastrointestinal helminth communities in vertebrate hosts from samples such as fecal pellets.

From 2023-2024 we successfully genotyped 57 snowshoe hare fecal pellet samples and 53 Appalachian cottontails collected in West Virginia with a ten microsatellite loci panel. Our analyses indicated that snowshoe hares in West Virginia exhibit low genetic diversity, high population structuring, and some sites exhibited elevated relatedness. Our density analysis showed that snowshoe hare population density ranged from 0.11 individuals/ha to 2.1 individuals/ha, falling into the low to moderate category of density estimates in the non-cyclic region of snowshoe hares’ range. Although Appalachian cottontails weren’t as rigidly genetically structured, they also exhibited low genetic diversity, and the southernmost site had elevated relatedness. Together, these findings suggest that both species in West Virginia may benefit from additional management attention such as habitat improvement to enhance connectivity among populations.

For the RHDV2 analysis, we obtained RHDV2 case counts for wild lagomorph species from 2020-2024 across 14 U.S. states from a publicly available USDA-APHIS dataset. We used Bayesian conditional autoregressive models to determine the effect of land cover and environmental factors on wild RHDV2 case counts. Our findings suggested that wild RHDV2 cases were positively related to RHDV2 cases in domestic lagomorphs, developed land cover, and lower annual precipitation. Our results also revealed very strong spatial dependence of RHDV2 cases. In West Virginia, our analysis suggests that disease surveillance should be extended to all directly surrounding counties if a RHDV2 case is detected in the state. Overall, this dissertation provides baseline data clarifying the conservation status of Appalachian cottontails and snowshoe hares in West Virginia, USA, investigated the factors that influence RHDV2 case counts in the Western US, created a tool to visually and quantitatively assess RHDV2 spread in West Virginia, and developed a user guide for using metabarcoding to characterize gastrointestinal helminth communities in vertebrate hosts.

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