Selection and demography are powerful forces that shape the evolution of populations, and these forces can be investigated in greater detail with the advent of genomic technologies for non-model organisms. Further, long-term population monitoring of wild populations of long-lived organisms can offer insight into the evolution of phenotypes and how populations change over time, which is of importance for vulnerable species. The following research presented in this dissertation assesses the roles of mate choice, demography, and genetics on phenotypic evolution across multiple scales, using experimental, population and species-wide comparisons in two long-lived ectotherms, the painted turtle (Chrysemys picta) and the western terrestrial garter snake (Thamnophis elegans).Certain phenotypes are the result of a complex interplay between natural selective pressures and sexual selection, such that phenotypes can both honestly signal health to potential mates and influence survivorship. In the first study, I assessed the role of adult painted color forelimb coloration as an honest signal of health status, measured through stress physiology and immune function, and found relationships between color and physiology were dependent upon sex and size in contrasting ways. In the second study, I assessed the relationships of various phenotypes, including color, stress levels, and sexually dimorphic traits, and reproductive success of adult male and female painted turtles in a semi-natural experiment with three adult sex-ratio treatments. Contrary to predictions, certain female phenotypes, including size and stress levels, were predictive of female reproductive success, but male phenotypes did not predict male reproductive success. These two studies represent some of the first tests of the function of color in adult painted turtles and suggest that female phenotypes may be the subject of male mate choice in painted turtles, contrary to former hypotheses of female mate choice in this species. Phenotypes that vary across populations of widespread species are often attributed to local adaptation to the disparate environmental conditions experienced across the species’ range. However, phenotypic plasticity can also contribute to phenotypic variation across populations, and genomic sampling can provide insight into the drivers of phenotypic variation. In the third study of my dissertation, I assessed population genomic variation across the western range of painted turtles to understand the contribution of local adaptation to the species’ distribution. I found that population genomic structure was consistent with serial founder effects from the eastern to the western United States, but found little evidence for genomic regions under different selective pressures across populations. Thus, while I could not exclude local adaptation, phenotypic plasticity is likely an important mechanism allowing painted turtles to colonize such a wide geographic range. Life-history traits can also be the result of local adaptation to disparate environments, even in the face of strong gene flow. With gene flow, local adaptation can be maintained through the combination of strong selection on individuals with traits mismatched to their environments and genomic architecture, including inversions, preventing recombination from breaking up favorable allelic combinations. In the fourth study of my dissertation, I investigated the genomics of life-history variation in populations of western terrestrial garter snakes in Lassen County, California. I found that despite recent gene flow among populations, there were regions of the genome that were strongly diverged between populations of the two life-history strategies, and many of these regions show patterns consistent with inversions. These regions contain genes related to many functions, including cellular senescence and the DNA damage-repair pathway, which support measured differences in these pathways between the two life-history strategies. Thus, both strong selection and genomic architecture play a role in the maintenance of these life-history strategies in these populations of long-lived reptiles.