Butterfly coloration has motivated the curiosity of research across many biological disciplines. It has especially been relevant in trying to address the basis of phenotypic variation. Research in this area has mainly focused on uncovering the genetic basis of such color patterning schemes, leaving the precise developmental pathways linking genotype to phenotype shrouded in mystery. The gene aristaless, which plays a role in appendage patterning and extension, has been duplicated in Lepidoptera. One copy, aristaless1 (al1), has been shown to control a white/yellow color switch in the butterfly Heliconius cydno, which suggests a novel function associated with color patterning and pigmentation. The second copy, aristaless2 (al2), has had some limited evidence showcasing a color patterning role. However, both copies lack previous research showing whether they still carry out the ancestral role related to appendage development. This highlights the need for the characterization of both ancestral and novel roles with the hope of better understanding how developmental mechanisms are able to bridge the gap between genotype and phenotype. In summary, across this dissertation, I analyzed novel and ancestral roles of al1 and al2 across multiple developmental stages and tissues of Heliconius cydno.First I investigated in Chapter 2 the developmental roles of al1 in embryos, larvae, and pupae using new antibodies, CRISPR/Cas9, RNAi, qPCR assays of downstream targets, and pharmacological manipulation of an upstream activator. Here I found that Al1 was expressed at the distal tips of developing embryonic appendages consistent with its ancestral role. In developing wings, I observed Al1 accumulation within developing scale cells of white H. cydno during early pupation while yellow scale cells exhibited little Al1 at this timepoint. Reduced Al1 expression was also associated with yellow scale development in al1 knockouts and knockdowns. As part of this chapter, I proposed a model for Al1 new color patterning function in which high levels of Al1 during early pupation, which are mediated by Wnt, are important for melanic pigmentation and specifying white portions of the wing while reduced levels of Al1 during early pupation promote upregulation of proteins needed to move and synthesize 3-OHK, promoting yellow pigmentation. Then in Chapter 3 I investigated the developmental basis of al2 and expanded on the expression and cellular characteristics of al1. Armed with our knowledge and tools from al1, I used newly developed antibodies targeting Al2 to analyze its expression profile within embryos. Similar to al1, al2 expression was observed in embryonic appendages showcasing again its expected ancestral role. However, a more careful analysis revealed a few distinct features between Al1 and Al2. Similar to what has been described in the previous chapter, Al1 was always found to be cytoplasmic (not co-localized with nuclei). Furthermore, its expression was higher earlier in embryonic development and faded as development continued. Al2, on the other hand, had lower expression earlier in embryonic development but did co-localize with nuclei. Al2 expression increased as embryonic development continued. Later in development, Al2 exhibited extranuclear expression but still retained its nuclear localization.