Bohannan, BrendanCaudill, Victoria2024-08-072024-08-07https://hdl.handle.net/1794/29839Evolution between species and within specific environments has resulted in a diverse array of traits and genetic variation. These are the result of interactions that have occurred across space and throughout time. As evolution progresses, it generates signals and patterns that can be used to unravel mysteries of the past and provide insight into future possibilities. By examining the signals left behind by the process of evolution, I have gained valuable insights onto what has occurred in the past. In chapter II, I use spatial simulations to explore the (co)evolutionary trajectories of levels of toxin resistance and toxin production in the predator-prey Thamnophis garter snake – Taricha newt system. Specifically, I examine how possi- ble genetic architectures of the toxin and resistance traits affect the coevolutionary dynamics by manipulating both mutation rate and effect size of mutations across many simulations. I find that coevolutionary dynamics alone were not sufficient in our simulations to produce the striking mosaic of levels of toxicity and resistance observed in nature. Instead, simulations with ecological heterogeneity (in trait cost- liness or interaction rate) did produce such patterns. In chapter III, I examined landscapes of genetic variation in cichlids, a species complex that has recently ra- diated. I used the phylogenetic relationship and population genetic measurements (mean nucleotide diversity and divergence) to describe large-scale variation across the genome. These patterns are likely caused by complex effects of inversions, in- trogression, and linked selection. Together, these findings contribute to building a strong foundation for understanding the evolutionary signals of natural selection and how its’ impacts vary along the genome. This dissertation includes previously published and unpublished co-authored material.This dissertation includes previously published and unpublished co-authored material.en-USAll Rights Reserved.Electronic Thesis or Dissertation