Illumination at the Intersections of Genomics and Public Health: A Study of Opsins, SPurS, Cluster Machine, and Ancestry in Genomics
Popejoy, Alice Beecher
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Light is essential to life on planet Earth, yet researchers know very little about how biology and health are influenced by this ubiquitous source of energy. Opsins comprise a large and diverse group of light-sensitive proteins that are conserved across all major branches of the tree of life, but their precise function in humans remains unknown. Studying these proteins is an important step in understanding the impact of light on human health, perhaps leading to a deeper understanding of connectivity of the brain and central nervous system to other major tissue systems of the body. The aims of this doctoral dissertation include a detailed evolutionary genomics study of opsins in vertebrates; a methods-development project designed to uncover novel interspecific signals of natural selection; and a survey of under-represented ancestry groups in genomics research. While the approaches and goals of each chapter in this dissertation are distinct, the underlying theme of this research is to employ existing methods (or design new ones) to probe topics that are often ignored or taken for granted, and to challenge outdated scientific assumptions and paradigms.