Date of Award

2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biology

Abstract

Much is still unknown about the impact and evolution of genomic variants. Genomic variants occur in all individuals and can be selected on by the environment. A polymorphic supergene composed of numerous inversions occurs on chromosome 2 of the white-throated sparrow (Zonotrichia albicollis). The supergene is present in both sexes and results in two morphological varieties, which differ in appearance, physiology, and behavior. This polymorphism is maintained through balancing selection due to disassortative mating between whites and tans. Though we understand the correlation between the supergene and morph, we do not understand the specific gene alterations. In thisdissertation, I use intra- and interspecies comparisons to identify putative variants and genes that may be involved in morph variation. I compared the genomes of the Zonotrichia genus to identify variants and better understand their origination. I found a large number of structural variants and single nucleotide polymorphisms among the Zonotrichia species. Through genomic comparisons to the rufous-collared sparrow (Zonotrichia capensis), I located scaffolds and genes with high levels of variation. These genomic regions make candidate locations for future intra- and interspecies comparisons. I also found a higher abundance of variants within select genes in chromosome 2 than in chromosomes 3 and 4 between Zonotrichia species. These differences suggest chromosome 2 is highly variable amongst closely related species. Finally, I identified morph differences within the expression of 12 genes on chromosome 3. Previously a relationship was hypothesized between chromosome 3 and the polymorphism. These genes provide a starting point for a more detailed investigation into the impact of chromosome 3 on morph. Together, this information is a step toward better understanding the Z. albicollis polymorphism. The complex nature of this polymorphism makes it difficult to study, but additional information may provide needed insight into the intricacies of genomic variation.

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