Animal development is not controlled by individual molecules.  Rather, it is controlled by very complex “genetic circuits” that translate abstract spatial and temporal information into morphological structures and physiological processes that make up a functional organism.  Each phenotypic trait is the end result of a complex series of interactions of multiple regulatory genes (such as transcription factors and signaling molecules) among themselves and with their downstream targets.  Although many individual components of this biological circuitry have been studied in detail, its overall organization remains elusive. 
The recent sequencing of several animal genomes has the potential to revolutionize our understanding of development.  With the identity, and often the molecular function, of every gene known or at least predicted, our attention is shifting from individual genes to complete developmental pathways.  The emerging  field of “developmental genomics” offers us a unique chance to understand animal development in all its complexity.
How is positional information interpreted by individual cells and translated into a structural or biochemical output?  How are multiple regulatory inputs integrated at the molecular level?  What is the regulatory logic that organizes thousands of component genes into a functional whole?  We use a combination of classical developmental genetics with the new genomic approaches to address these and other questions in the fruit fly Drosophila melanogaster.  Our favorite models are pigmentation (because it’s simple), sex comb development (because it’s complex), and sensory system development (because it’s really complex…).

    Females and males of many animal species differ in their morphology, physiology, and behavior.  Well, vive la différence,  - but how are these differences produced?  What genetic and developmental mechanisms are responsible for generating the distinctions between males and females?  In insects, somatic sex determination is cell-autonomous, i. e. the sex of each cell is determined independently of its neighbors.  Actually, it’s very simple to construct a fly that is part male and part female.  Unfortunately, we know very little about the genes and developmental pathways that control sexually dimorphic differentiation of specific tissues and organs.  The traits we study – pigmentation, sex combs, and sensory systems – are all sexually dimorphic, and one of our goals is to identify the genetic inputs responsible for producing this dimorphism.

    A synthesis of evolutionary and developmental biology is an exciting  new field that is giving us a new understanding of both development and evolution.  On the one hand, an explicitly evolutionary approach allows us to put animal development in a historical context.  The complexity of modern animal development is a reflection of their long and eventful past.  Each development pathway has evolved by a gradual assembly from individual genes, and many pathways continue to evolve: losing old components, acquiring new ones, and changing  their properties and functions.  This process is reflected in the origin of new morphological traits: different animals look different because the underlying developmental processes have diverged.  This is the flip side of the “Evo-Devo” synthesis: by applying ideas and techniques from developmental biology, we can understand the molecular mechanisms of evolutionary change.
    What changes in DNA sequences are responsible for morphological, physiological, and behavioral innovations?  How do developmental pathways evolve?  How is molecular divergence translated into phenotypic diversity?  We tackle these questions using the same experimental models that we use to study developmental genomics:  pigmentation and sex comb development.  Over 50 Drosophila species that we keep in the lab provide us with a wealth of developmental variation to explore.

    All differences between organisms, no matter how dramatic, originate as genetic variants within natural populations.  At some point, humans and cockroaches shared a common ancestor, and that’s a humbling thought.  Developmental and morphological variation accumulates gradually under the influence of selection, genetic drift, and geographic isolation, leading to the origin of new species and new phenotypic traits.  To understand the forces and processes involved in the divergence of nascent species, we turn to the analysis of genetic and developmental variation within species and among recently diverged species.
    Our favorite model is the Drosophila bipectinata species complex – a group of four closely related species that live in the rainforests (and, truth be told, the garbage dumps) of Southeast Asia.  These species combine very low genetic divergence with a high degree of morphological and behavioral differentiation, making them an ideal model for microevolutionary studies.  We combine developmental biology with quantitative and population genetics and field work in an effort to identify the genetic changes responsible for the origin of developmental and morphological variation.