Date of Award

Fall 2026

Abstract

Our understanding of gene and gene family evolution has advanced rapidly in recent decades thanks to the prolific expansion of available sequence and genomic data for non-model species. While these resources enable deeper and more complex phylogenies of gene evolution, maintaining good input sequence alignment quality and computational efficiency requires us to select which genomic sequences are most relevant. Instead of using subjective criteria, this dissertation emphasizes a novel, phylogeny-first method for selecting input sequences called Phylogenetic Focusing. Chapter One introduces this program and explains how its six major steps enable sequence selection in a phylogeny-based manner, helping ensure subsequent gene trees capture as broad a range of relevant data as feasible. We further assess PhyFocus by comparing the program's output against test iterations that toggle key pipeline variables and find that PhyFocus succeeds in limiting input sequence data according to phylogenetic evidence, providing effective trade-offs in runtime and overall quality relative to both more restrictive and relaxed approaches. The remainder of this dissertation focuses on investigating the evolution of sensory systems by applying PhyFocus. Chapter Two is an introductory review of ten major gene families that comprise many of the chemosensory genes in metazoans. For each major gene family, this chapter provides foundational details for their discovery and function, major conserved sequence elements, canonical signaling pathways, and published phylogenetic relationships. This context is then leveraged for Chapter Three, which applies PhyFocus to each of these 10 chemoreceptor families in order to further clarify their evolutionary relationships and origins. Our phylogenies provide a metazoan-wide perspective on the extensive impacts of gene duplication in chemoreceptor evolution, and lend greater support to many of the previously hypothesized relationships and origins for these gene families. Finally, Chapter Four applies PhyFocus to the metazoan Phosphodiesterase (PDE) superfamily, a group comprised of 11 gene families that all regulate cyclic nucleotide mediated signaling and have extensively diverse biological impacts. We further focus on vertebrate PDE6, the only PDE involved with the sensory modality of vision. As in Chapter Three, our phylogenetic results provide a species-rich perspective that supports many of the established phylogenetic relationships; for PDEs, our data also emphasizes the impact of whole genome duplication events in vertebrates, including for PDE6. We further find that the evolution of phototransductive PDE6 in vertebrates is correlated with the conservation of numerous unique residues in the protein sequence, and may be related to the vertebrate-specific co-evolution of the PDE6 gamma inhibitor.

Document Type

Dissertation

First Advisor

David C. Plachetzki

Second Advisor

Rick Cote

Third Advisor

Matthew MacManes

Department or Program

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

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