Theses and Dissertations

ORCID

https://orcid.org/0000-0003-3963-7060

Advisor

Dapper, Amy

Committee Member

Gout, Jean-Francois

Committee Member

Welch, Mark

Committee Member

Hoffmann, Federico

Date of Degree

5-15-2026

Original embargo terms

Immediate Worldwide Access

Document Type

Dissertation - Open Access

Major

Computational Engineering

Degree Name

Doctor of Philosophy (Ph.D.)

College

Office of Academic Affairs

Department

Computational Engineering Program

Abstract

Sexual reproduction is an important driver of genetic diversity and speciation through such forces as selection, mutation, and drift. Sauropsids are an appropriate clade to study shared molecular drivers of sexual and genomic evolution due to their genome architecture, sex determination mechanism (SDM) plasticity, and large syntenous genomic regions. Using comparative phylogenetic methods, I identify predictable patterns of selection in meiotic recombination genes and clade-specific drivers of recombination rate evolution. Then, leveraging whole genome sequencing, I demonstrate that American alligator genomes are characterized by an ancient loss of genetic diversity driven by drift and historic inbreeding. I also generate a fine-scale recombination landscape for alligators, motivating further investigation into the unique recombination landscapes of crocodilians. Lastly, I combine phylogenetic comparative methods with physical and life history trait data to reconstruct ancestral SDMs for sauropsids, infer a bidirectional transition network between genetic and temperature dependent sex determination, and explored patterns of selection shaping the evolution of and transitions between SDMs, identifying no significant patterns of adaptive evolution between sauropsid lineages. Thus, while I identified predictable patterns of molecular evolution acting on the meiotic recombination pathway, the presence of shared genome architecture is not synonymous with a shared function. Studying these mechanisms at the molecular level, within panels of focal genes, and within the population genetics of a focal species with a remarkable population genetics history, allows us to contextualize the forces driving the genetic background and adaptive potential of species in a changing world.

Sponsorship (Optional)

National Science Foundation CAREER 2143063

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