The origin of evolutionary novelty involves changes across the biological hierarchy: from genes and cells to whole organisms and ecosystems. Understanding the mechanisms behind the establishment of new designs involves integrating scientific disciplines that use different data and, often, different means of testing hypotheses. Discoveries from both paleontology and developmental genetics have shed new light on the origin of morphological novelties. The genes that play a major role in establishing the primary axes of the body and appendages, and that regulate the expression of the genes that are responsible for initiating the making of structures such as eyes, or hearts, are highly conserved between phyla. This implies that it is not new genes, per se, that underlie much of morphological innovation, but that it is changes in when and where these and other genes are expressed that constitute the underlying mechanistic basis of morphological innovation. Gene duplication is also a source of developmental innovation, but it is possible that it is not the increased number of genes (and their subsequent divergence) that is most important in the evolution of new morphologies; rather it may be the duplication of their regulatory regions that provides the raw material for morphological novelty. Bridging the gap between microevolution and macroevolution will involve understanding the mechanisms behind the production of morphological variation. It appears that relatively few genetic changes may be responsible for most of the observed phenotypic differences between species, at least in some instances. In addition, advances in our understanding of the mechanistic basis of animal development offer the opportunity to deepen our insight into the nature of the Cambrian explosion. With the advent of whole-genome sequencing, we should see accelerated progress in understanding the relationship between the genotype, phenotype, and environment: post-genomics paleontology promises to be most exciting.
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