Graduation Year

2025

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Integrative Biology)

Major Professor

Mark J. Margres, Ph.D.

Committee Member

John E. Parkinson, Ph.D.

Committee Member

Yusan Yang, Ph.D.

Committee Member

Andrew Storfer, Ph.D.

Keywords

Genomics, Islands, Proteomics, Rattlesnakes, Transcriptomics, Venom

Abstract

A central challenge in evolutionary biology is understanding how genetic variation leads to phenotypicdiversity, particularly for complex traits that strongly influence fitness. Traits form the substrate of natural selection, but it is genes, that are inherited across generations. To fully understand the evolutionary process, we must therefore connect the molecular basis of trait variation with the evolutionary outcomes of such traits.

For relatively simple traits, the genotype–phenotype relationship is well understood. Classic systems, such as coat color in beach mice or toxin resistance in garter snakes, have provided effective examples of how relatively few loci underlie conspicuous adaptive differences across populations and species. Yet most traits central to fitness are more complex, being influenced by many genes; such increases in complexity may result in the manifestation of pleiotropic constraints, epistatic interactions, and additional context–dependent gene–environment interactions absent (or nearly so) from simpler phenotypes. The architecture of complex traits makes them both more difficult to study and to predict. Yet understanding their evolution remains a central goal in evolutionary biology, as most traits of significance for ecology, evolution, conservation, and disease are inherently complex.

Snake venom provides an exceptional system for addressing this challenge. Venom is a complex molecular phenotype, composed of 40–100 proteinaceous toxins. Venom is ecologically important, as snakes rely on venom to capture and subdue prey, and its function is directly related to species interactions. All genes producing toxic proteins as part of the venom phenotype are expressed exclusively in specialized venom glands, reducing pleiotropic effects, and most toxin families and genes are well characterized. Snake venom is therefore sufficiently complex to explore the dynamics of complex trait evolution, while remaining genetically tractable.

Extensive work has shown that snake venoms evolve under strong selection, often linked to diet. Yet it remains unclear whether venom evolution, and by extension the evolution of complex traits involved in species interactions, follows predictable patterns across ecological and biogeographic contexts. My dissertation addresses that gap by leveraging venom as a model to test the predictability of complex trait evolution, examining patterns of venom variation across rattlesnake species and populations.

For my first chapter, I generated a reference-quality genome and range-wide genomic, transcriptomic, and protein data for the red diamond rattlesnake (Crotalus ruber) to identify the principal axes of venom variation in this species: neutral population structure, geographically variable (a)biotic factors, or life history. Although neutrality accounted for part of the observed variation, ontogeny emerged as the dominant axis. Such a pattern is consistent with observations in other rattlesnake species, where developmental shifts in venom expression comprise the largest axes of venom expression variation and correspond with changes in diet. The results of this chapter highlighted the importance of explicitly modeling both neutral and putatively adaptive processes to identify evolutionary regimes of venom variation, and indicated that venom is evolving under strong selection, most likely in response to dietary changes across life history.

For my second chapter, I investigated whether ontogeny, identified as the dominant axis of venom variation, could be co-opted across geographic space, particularly when populations colonize novel environments. On Isla Cerralvo, populations of the Baja California rattlesnake (Crotalus enyo) exhibit smaller heads than their mainland counterparts, likely reflecting constraints on prey size in island environments. Because of this morphological shift, I predicted that island snakes might also exhibit a juvenile–like venom phenotype, representing a parallel evolutionary change in venom and head morphology. I compared venom expression across size classes in island and mainland populations. Whereas mainland snakes exhibited the expected ontogenetic shift, island snakes expressed a juvenile–like venom phenotype independent of age. The results of this chapter demonstrated that evolution in novel and isolated environments can proceed rapidly by repurposing pre–existing axes of variation, in this case ontogeny, and reinforced the functional integration of venom with morphology in a complex, feeding phenotype.

Having demonstrated in Chapters 1 and 2 that venom evolves under strong selection, likely driven by diet, and that such changes can occur rapidly in island environments, in Chapter 3 I asked whether these patterns could be generalized into a predictive framework across multiple populations and species. To evaluate the predictability of venom complexity on a broader scale, I applied Island Biogeography Theory (IBT), which explains patterns of species richness based on island characteristics. Venom complexity, defined as the number and relative abundance of unique venom proteins, has been shown to correlate with phylogenetic diet diversity, a proxy for ecological breadth. I quantified venom complexity in 83 individuals from four species of rattlesnakes across 11 Gulf of California islands using the Shannon Diversity Index (H) and modeled its relationship with characteristics of IBT that predict species richness: island area, isolation, and age, as well as the number of congeneric competitors. I found that venom complexity was negatively correlated with area, isolation, and competition. Isolation followed IBT expectations, but the negative relationship with area contrasted with my predictions, a pattern reinforced by competition emerging as the strongest predictor. The results of this chapter suggested that ecological processes such as niche partitioning and specialization drive venom complexity evolution in addition to habitat isolation. Importantly, these results show that complex molecular phenotypes involved in species interactions can evolve in predictable patterns that coincide with biodiversity, and that both direct interactions, such as predator–prey dynamics, and indirect interactions, such as competition, play crucial roles in shaping complex trait evolution.

My dissertation leverages rattlesnake venom, a genetically tractable yet complex phenotype with a well– established genotype–phenotype–fitness link, to demonstrate that patterns of variation in complex traits can be predicted from ecological and biogeographic contexts. By integrating genomics, transcriptomics, proteomics, and ecological theory, this work advances a broader eco-evolutionary framework in which biodiversity patterns, including those predicted by IBT, can be used to predict the evolution of complex traits. As human-mediated environmental change continues to alter natural ecosystems, this framework offers a foundation for predicting how habitat and biodiversity loss alter the evolution of traits central to survival and ecological interactions.

Download

Share

COinS