Date of Award

Summer 7-2023

Degree Type

Masters Thesis

Degree Name

Master of Science (MS)


Biological, Environmental, and Earth Sciences

Committee Chair

Alex Flynt

Committee Chair School

Biological, Environmental, and Earth Sciences

Committee Member 2

Nicole Phillips

Committee Member 2 School

Biological, Environmental, and Earth Sciences

Committee Member 3

Dmitri Mavrodi

Committee Member 3 School

Biological, Environmental, and Earth Sciences


The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population structure, and assess genetic health. In addition, researchers can examine unique features of genes related to the health of a threatened species, such as genes involved in immune function, reproduction, environmental response, as well as evolutionary trends and niche adaptations.

Recent developments in sequencing and software also allow researchers to examine the noncoding- “ome”, providing a glimpse into gene regulation, developmental pathways, and response to viral sequences and mobile elements. Characterization of the biogenesis pathways of noncoding RNAs has facilitated the development of RNA interference strategies which are increasingly being used in therapeutics, agriculture, and pest control. The focus of this project is to use available sequencing technology and computational methods to annotate the genome and small RNA pathways of non-model organisms.