DOI

https://doi.org/10.25772/9D3M-Z460

Defense Date

2022

Document Type

Thesis

Degree Name

Master of Science

Department

Bioinformatics

First Advisor

Lesley Bulluck

Abstract

In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs associated with local adaptation, and a partial redundancy analysis (pRDA) to identify SNPs associated with site-specific environmental factors. I then performed an exploratory gene ontology analysis of the top ten outliers identified from both methods. I found two of the top outliers both fell within gene structures that aligned to proteins localized to the eye, which I suggest may be due to selective pressure on the visual system of the Prothonotary Warbler, perhaps due to sexual selection or adaptation to light pollution. Further investigation is needed to determine whether this signal is not a false positive, and if so, determine what selective pressures are acting on the Prothonotary Warbler visual system. There did not appear to any other discernible patterns in the gene ontologies of the top outlier SNPs, but a full gene ontology analysis may be able to reveal additional selective pressures for further investigation.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

12-15-2022

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