Evolutionary developmental biology (evo-devo) seeks to unravel the bases of developmental changes in body plan evolution of complex organisms such as animals and plants. The significance of this relatively new discipline is based on the premise that evolution cannot be fully understood without understanding the evolution of developmental programmes , and a number of novel conceptual frameworks have emerged from evo-devo research to supplement those of traditional evolutionary biology, such as DEVELOPMENTAL REPROGRAMMING [1–6]. The latter concept describes the process that acts between mutation and selection on the level of the organism, leading from an altered gene product to a new ontogeny and phenotype. Reprogramming has been proposed to constitute an additional evolutionary mechanism because some ontogenetic changes may be promoted by existing developmental mechanisms while other alterations are prevented [1, 3, 7] (referred to as 'developmental drive' and 'constraint', respectively ). It seems therefore likely that evolution can be biased by development, and this may have a powerful impact on the direction of evolutionary change [1, 7, 8].
During the past two decades it was discovered that most animals, no matter how divergent in form, share specific gene families that regulate major aspects of body patterning, for instance many homeobox-containing genes [9, 10], which are even present in the Cnidaria . Recent findings show that morphologically simple organisms often possess genes, such as members of the pax gene family, that are homologous and show a high level of sequence similarity to those of higher vertebrates [12–15]. Despite this astonishing extent of evolutionary conservation in developmental regulatory genes across major taxonomic groups, there are also cases where gene expression patterns differ markedly among closely related taxa, for instance in the molecular mechanisms that determine the spatial axes of the tetrapod limb . In the recent past, one of the goals of evo-devo research was to search for putative phylum-specific genes, which may have given rise to phylum-specific evolutionary novelties. However, the view hat new phyla arose in concert with the advent of novel genes has been increasingly challenged [17, 18]. Instead, there is mounting evidence that the evolution of lineage-specific body plans does not primarily depend on the invention of new genes but rather on the deployment of new gene regulatory circuitries. Changes in the transcriptional regulation of genes may thus be more significant than changes in gene number or protein function [18, 19]. Moreover, the use of 'old' genes for novel structures has recently been demonstrated in a number of instances [20, 21].
Among the main controversies that have emerged from evo-devo research is whether or not the utilization of conserved molecular components in developmental programmes across animal phyla can be taken as evidence for a shared developmental function in their latest common ancestor. The alternative would be the co-option of conserved genes and gene pathways to new functions, most likely operating in non-homologous structures. It is therefore fundamental to employ phylogenetic methods and homology criteria meticulously to resolve such issues, including the idea of retention of genetic programmes or 're-awakening' [22–25]. Recent gene expression studies, for instance, have revealed some common molecular aspects of segment ontogenesis between insects and annelids (shared segmental expression of engrailed and wingless) , and between arachnids and chordates (shared role of the notch signalling pathway) , which have been used to reinforce the hypothesis that the last common ancestor of all bilaterian animals was segmented [17, 28–30]. However, one must be particularly critical about such deep homologies since the probability of gene recruitment to non-homologous roles grows with phylogenetic distance [1, 31]. The use of gene expression patterns to establish homologies between morphologically similar features among distantly related organisms is another matter of ongoing debate [1, 31, 32].
In this review, we provide a brief introduction to evolutionary developmental biology for newcomers to the field who may be overwhelmed by the abundant literature. We outline how recent advances in evo-devo research have changed our understanding of the genesis of species differences and morphological novelties. In particular, we present examples to show that the contribution of phylogenetics to test hypotheses for the interpretation of problems in the evolution of developmental processes [20, 33, 34] is becoming more and more recognized. We also stress the importance of accurately assessing homology relationships and appropriate phylogenetic sampling of organisms for evo-devo studies.