Many animals are built from reiterated parts, such as the segments and appendages of arthropods and the somites and vertebrae of vertebrates. During evolution there has been a trend toward the divergence of the number, morphology, and function of these parts, both within and between animal taxa. Deciphering the genetic regulatory mechanisms that control the formation, number, and ultimate morphology of body parts is therefore crucial to understanding the dual mysteries of the development and evolution of animal design.
The fruit fly Drosophila melanogaster has emerged as a key model system for elucidating the genetics and molecular biology of animal development. Advances in our knowledge of how this complex animal develops have made possible comparative studies to identify common features of animal design and to determine how morphological diversity evolves. Our laboratory has worked toward a detailed mechanistic understanding of some of the major features of Drosophila development. This has provided the foundation for the study of the genetic and developmental basis of animal diversity, as well as new insights into animal origins and relationships. This approach has resulted in a deeper understanding of how developmental genes and patterning mechanisms evolve and has uncovered some of the first direct evidence for the central role of changes in the regulation of genes in the diversification of body plans and body parts and in the origin of new structures and pattern elements.
The Control of Genetic Networks by Selector Genes
In Drosophila, adult appendages develop from imaginal discs that give rise to both body wall structures and the appendages. Eyes, wings, legs, antennae, and other structures are derived from these sacs of cells, which undergo extensive growth and morphogenesis during the larval and pupal stages. Transcription factors encoded by selector genes control the formation and patterning of these body parts. Two types of selector proteins are of special interest: the field-specific selectors are required for formation of a particular structure from a developmental field, and the Hox proteins act to differentiate homologous structures (fore- and hindwing; legs) from each other.
Drosophila is a two-winged insect that evolved from a four-winged ancestor. Its hindwings have been greatly reduced and modified to act as balancing organs (halteres) during flight. Drosophila wings and halteres are serially homologous structures, and the differences between these structures are regulated by the product of the Ultrabithorax (Ubx) gene. We have identified genes in the wing-patterning network that are directly regulated by Ubx in the developing haltere. The critical feature of this control is the presence of Ubx-binding sites in cis-regulatory elements that also integrate inputs from the Vestigial/Scalloped selector proteins and signal transduction pathways.
The Evolution of Animal Design
How do body plans and body parts evolve? Differences in morphology are, of course, the developmental products of genetic differences between animals, but it has not been clear how many or what kinds of differences underlie changes in body patterns. Early investigations into the nature of genetic evolution proposed two potential mechanisms for the origin of new features: gene duplication and divergence, and regulatory changes in gene expression.
With an expanding understanding of the genes that control body pattern in model animals, it is now possible to investigate the genetic basis of morphological diversity in related animals. The major architectural differences between insects and other arthropods involve variations in the number, type, and pattern of segments and body appendages. Comparisons of how genes are used in different animals, such as diverse insects, centipedes, and crustacea, have revealed the primacy of regulatory changes in the generation of morphological diversity. Regulatory changes in developmental programs are by far the more common mechanism in the evolution of body plans and body parts than is the evolution of new genes. However, we have also found, quite unexpectedly, that functional changes have occurred in certain Hox proteins in the course of arthropod evolution.
A major challenge before us is to elucidate how genetic regulatory circuits evolve and to understand the roles of selection and genetic variation in their evolution. Molecular studies of Hox-regulated target genes suggest that these changes occur through accumulation of mutations in regulatory DNA sequences. Because it is very difficult to dissect these mechanisms over great taxonomic distances, we have bridged this gulf between large-scale evolutionary change and the evolutionary mechanisms operating within species by developing several experimental models of the evolution of characters among closely related Drosophila species, primarily models involving pigmentation of the body and wings. We have also shown how the gain and loss of binding sites for Hox proteins in the regulatory elements affect the evolution of body pigmentation.
Melanic pigmentation patterns differ widely across Drosophila species, from no pigment to complex patterns of stripes and spots, to ubiquitous black coloration. We have identified several of the key genes and molecular genetic mechanisms that have contributed to this divergence. One of the most remarkable trends in the evolution of pigmentation patterns is the repeated, independent occurrence of similar patterns on fly bodies and wings. We have uncovered instances where similar patterns have evolved independently (parallel evolution) via changes at the same gene as well as via different loci. The examples offer some unique insights into mechanisms that shape what patterns are most readily produced.
One of the major forces appears to be the existence of evolutionarily stable "prepatterns" of transcription factor distribution. Regulatory proteins that serve in one or more regulatory circuits can be exploited in the generation of new patterns. The similarity of "cryptic" prepatterns among related species makes the evolution of similar overt patterns more probable.
We have elucidated part of the genetic regulatory circuit that controls sexually dimorphic abdominal pigmentation and traced the evolution of this circuit through the evolution of the Drosophila subfamily. Our studies suggest that the expression of Hox proteins constitutes another cryptic set of prepatterns. Moreover, these studies illustrate how more complex Hox-regulated traits diverge at higher taxonomic levels.
Adaptation and Gene Evolution
The evolution of regulatory sequences appears to be the major mechanism underlying the evolution of animal form. However, several genetic mechanisms—including the evolution of protein-coding sequences and gene duplication, as well as the evolution of regulatory sequences—are sources of variation in all species and contribute to organismal adaptation. We are keen to understand, in general, the contribution of these mechanisms to evolution and adaptation, and the origin of novel properties. Because natural selection can operate on very small differences in performance, it is critical to develop methods for detecting slight differences in molecular function and the signature of natural selection. We have developed new experimental platforms using various yeast species as models to explore molecular and organismal evolution.
For several decades, much attention has been placed on gene duplication as a source of new gene functions. More recently, however, it has become appreciated that after gene duplication, the resulting duplicates are often "subfunctionalized" and accumulate complementary mutations: the two genes together perform the function formerly carried out by a single ancestral gene. Gene duplication, therefore, is only a necessary contributor to adaptation if it enables previously unfavored mutations to evolve. We have identified one such instance in a bifunctional yeast gene where gene duplication enabled the two functions to become independently encoded and regulated and where most of the adaptive divergence between the two duplicates involved regulatory sequences. Our findings suggest that coding sequences and regulatory sequences that harbor more than one function may require duplication in order for an individual function to evolve.
