Theses and Dissertations

Advisor

Morin, Dana

Committee Member

McConnell, Mark

Committee Member

Davis, J.

Date of Degree

8-7-2025

Original embargo terms

Immediate Worldwide Access

Document Type

Graduate Thesis - Open Access

Major

Wildlife, Fisheries, and Aquaculture

Degree Name

Master of Science (M.S.)

College

College of Forest Resources

Department

Department of Wildlife, Fisheries and Aquaculture

Abstract

Swamp rabbits (Sylvilagus aquaticus) are a potentially useful indicator species for bottomland hardwood forest ecosystem health and can be monitored using fecal pellet surveys. Advances in genetic sequencing technology have allowed researchers to obtain genetic information about wildlife using non-invasive sampling. Genotyping-in-thousands by sequencing (GT-seq) allows researchers to target specific genetic markers selected to meet their objectives, such as differentiating individuals. We investigated the utility of GT-seq for genotyping DNA derived from swamp rabbit fecal pellets. We designed a GT-seq panel for swamp rabbits, then tested the panel on fecal samples collected in the Mississippi Delta. We developed a real time polymerase chain reaction assay to compare target DNA concentrations to GT-seq genotyping success. We also investigated population structure among three swamp rabbit subpopulations in Mississippi. The GT-seq panel effectively differentiated among individuals in Mississippi when samples were genotyped at 26 or more loci but performed poorly overall on fecal samples.

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