Date of Award

Spring 2024

Project Type

Dissertation

Program or Major

Genetics

Degree Name

Doctor of Philosophy

First Advisor

David Plachetzki

Second Advisor

W. Kelley Thomas

Third Advisor

Matthew MacManes

Abstract

Advances in sequencing technology have facilitated a surge in the production of genome data for diverse animal species. Researchers are presented with the opportunity to create comprehensive phylogenomic datasets, which have previously not been feasible. Unfortunately, extracting biologically relevant information from such a large amount of data is time consuming and computationally expensive, often limiting the scope and possibility of such analyses. My Ph.D. research aims to establish a methodological framework for investigating questions of biological function using comparative genomic and phylogenetic methods. Using two different metazoan genomic datasets we demonstrate the wide-ranging applicability of this framework by addressing research questions at three vastly different biological scales. On the level of a multi-protein macromolecular complex, in chapter one, I use this approach to identify the forces that keep the kinetochore, a critical cellular structure functioning properly even as external selective pressures act on the individual components. In chapter two, I expand the study system beyond a single cellular complex to encompass the many facets of visual sensation in mammals and highlight genes which could be important for vision adaption to diverse photic environments. Lastly, on a macroevolutionary scale, chapter three elucidates the large-scale genome changes accompanying the evolution of Cnidaria, one of the oldest branching groups of animals including the species that form our coral reefs which are increasingly threatened by rising ocean temperatures. Taken together this work illuminates the molecular underpinnings of functional biological innovation and presents a tangible workflow for similar analyses which can take advantage of the valuable genomic resources we now have at our disposal.

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