Year of Award

2025

Document Type

Thesis

Degree Type

Master of Science (MS)

Degree Name

Ecology and Evolution

Department or School/College

Division of Biological Sciences

Committee Chair

Dr. Jeffrey Good

Commitee Members

Dr. Zac Cheviron, Dr. Andrew Whiteley, Dr. Douglas Emlen

Keywords

Whole genome, noninvasive, fecal, preservation, Lepus americanus

Subject Categories

Ecology and Evolutionary Biology | Genetics and Genomics

Abstract

Genomic analyses can provide powerful insights into important issues in conservation biology, including rapid estimates of overall genetic diversity and related population genetic parameters. Noninvasive DNA sampling from fecal samples is an affordable, efficient, and broadly applicable sampling method that has been used in many targeted genetic analyses. However, the efficacy of whole genome sequencing from fecal samples remains relatively unexplored in most taxa. Here, we present results from two experiments designed to test the quantity and quality of whole genome resequencing data obtained from snowshoe hare (Lepus americanus) fecal pellets. Extensive previous research has used genetic analyses to inform studies of population ecology, life history, environmental adaptation, and conservation management of this important North American species. Thus, hares provide an amenable study system to explore the potential and limits of genome sequencing from fecal material. In Chapter 1, we used captive hares to deploy a 10-day experimental time course, testing the effects of sample age on the recovery of host DNA, and the suitability of fecal samples for genome-wide genotype inferences when compared to tissue samples from the same individuals. We found that fecal samples were ~ three to five times less efficient than tissue-based sequencing, but yielded comparable data within a range of sequencing efficiency that is likely to be experimentally tractable for many researchers. In Chapter 2, we used a field application to test the effects of preserving fecal samples in ethanol or silica on genome-wide genotype inferences. We found that more DNA was recovered from fecal samples preserved in silica. However, genome-wide genotype information from both fecal preservation methods replicated population genetic inferences into sample relatedness and genetic diversity that were highly similar to tissue-based inferences from the same hare. Given these results and that silica is more cost-effective and easier to deploy in the field, silica-based preservation is likely to be the optimal methodology for most applications. These genome sequencing experiments provide important insights for researchers interested in recovering genomic data from noninvasive samples of snowshoe hares and other species.

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© Copyright 2025 Jessica J. Powell