Understanding how novel traits evolve is a central question in evolutionary biology. However, unraveling the complex genetic and developmental mechanisms underlying trait innovation can be challenging, especially when the trait evolved a long time ago. One approach to this complexity is to leverage natural polymorphisms, revealing variation in the expression or function of novel traits. Polymorphisms can provide insights into the origin, maintenance, and diversification of trait innovation, and the evolutionary forces and constraints shaping them. Sex-limited polymorphisms, a special class of polymorphism in which only one sex exhibits variation in the trait, can be particularly informative because they allow for the investigation of not only the genetic basis and evolutionary history of novel traits, but also how differences between sexes (sexual dimorphisms) are regulated and evolve.

In my thesis, I utilize naturally occurring female-limited color polymorphisms to answer questions about the evolutionary origin, mechanism, and maintenance of wing coloration and patterning variation in butterflies.  Butterfly wing coloration and patterning are not only striking examples of morphological diversity but also critical to survival and fitness. While butterfly wing patterning and coloration have inspired evolutionary thinking  for over a century, they have recently become a model system for Evo-Devo research. As easily visually assessed traits, butterfly wings have proven perfect candidates for more recent advances in Evo-Devo, acting as a template for understanding the function, recruitment, and evolution of gene regulatory networks (GRNs) generating complex phenotypes. 

In Paper I, I reconstruct the evolutionary history of Alba, a genetically determined female-limited alternative life history strategy, found in over one third of species in the genus Colias (Pieridae). In this polymorphism, some Colias females redirect resources from wing coloration to reproductive development, resulting in white rather than orange wings. I show this polymorphism evolved once in the Colias phylogeny through a transposable element insertion and has persisted for over a million years through balancing selection and introgression. In Paper II, I dissect the pteridine biosynthesis pathway, a pigment that Pierid butterflies, including Colias, use to color their wings. I highlight not only the extent of pteridine use by Pierid butterflies, but also evidence suggesting novel evolution for core components of the biosynthesis pathway. In Paper III, I investigate the genetic basis of a regionally isolated sexual dimorphism in Pieris napi, called adalvinda. Rather than the creamy white wings seen in the rest of the range, females in northern Scandinavian populations have highly melanized, almost dark brown wings. Similarly to Paper I, I in Paper III identify a transposable element insertion, but this time upstream of the gene cortex associated with female wing melanization. This finding contributes to a growing body of literature linking cortex with butterfly wing melanization, while emphasizing the potential role transposable elements may play in the evolution of novel – and especially female-limited or sexually dimorphic – traits. Lastly, in Paper IV, I present a new reference genome for the Edith's Checkerspot butterfly, offering an important resource for future functional genomic and conservation analyses, and demonstrating an efficient framework for developing genetic resources for non-model systems. 

In summary, my thesis demonstrates the powerful potential of utilizing naturally occurring polymorphisms or induced mutations to study the evolution of novel traits.