Revealing the Structure and Evolution of a Fruit Fly Gene Regulatory Network by Varied Genetic Approaches

Date of Award


Degree Name

Ph.D. in Biology


Department of Biology


Thomas Williams


There are 36 recognized animal phyla that are characterized by a set of morphological features considered to be a body plan. Upon these 36 body plan themes, there has evolved an interminable amount of diversity ranging from the underwhelming and simplistic to the most extraordinarily ornate. These body plans and the diverse traits that decorate them are the products of orchestrated gene expression during the developmental process. Underlying the development of morphological traits is a hierarchy of regulatory gene expression, chiefly comprised of transcription factor proteins, organized into a gene regulatory network (GRN) that ultimately impart instructions on so-called differentiation genes responsible for building the physical trait. Expression for genes within the GRN is controlled by cis-regulatory elements (CREs), which instructs a gene as to when and where it is to be active during development and how much of the protein product it encodes for is needed. The goal of my thesis research was to understand how changes to a GRN drive the development and evolution of animal morphology. Chapter 2 presents research on the repeated evolution of male-specific abdominal pigmentation in fruit fly species of the Sophophora subgenus. This research focused on analyzing the phylogenetic distribution of male-specific pigmentation and characterizing the expression for genes involved in the pigment metabolic pathway. We found dimorphic pigmentation to be widespread among distantly related fruit fly species. Using in situ hybridization and immunohistochemistry, we show that there is conservation in the expression of the pigmentation enzymes responsible for constructing the trait and flexibility at the level of the regulatory genes that control their expression. In Chapter 3, we investigate the extent to which mutations within the CREs (cis-evolution) or the CRE-interacting transcription factors (trans-evolution) for pigment metabolic enzymes contribute to the origin, diversification, and loss of sexually dimorphic pigmentation among fruit fly species of the Sophophora subgenus. This research focused on CREs for the differentiation genes yellow and tan, which independently evolved a male-specific pattern of regulation. Using reporter transgenes in four species backgrounds, we found that both cis- and trans-evolution contributed to the origin and loss of dimorphic pigmentation, while diversification was a result of trans-evolution alone. Chapters 2 and 3 illustrate a significant role for changes to the regulatory tier of the Drosophila pigmentation GRN in the evolution of the diverse patterns that adorn the abdomens of fruit fly species. However, identifying which genes have changed and where they lie within the network remains a daunting task due to our lack of a comprehensive understanding of which transcriptions factors comprise the regulatory tier of this network. In Chapter 4, we utilized RNA interference (RNA-i) to reduce the expression of 571 unique transcription factor proteins in the model species D. melanogaster. We identified 37 novel transcription factors to occupy the regulatory tier of the pigmentation GRN. Future work should focus on elucidating the CRE interactions for these genes to determine their regulatory linkages within the GRN.


Biology, Evolution and Development, Genetics, transcription factor, gene regulatory network, cis-regulatory element, Drosophila, pigmentation, evo-devo, morphology, dimorphism, convergence

Rights Statement

Copyright 2021, author.