role of developmental genetics in understanding homology and morphological evolution in plants

Homology assessments are critical to comparative biological studies. Although gene expression data have been proposed as instrumental for defining homologous relationships, several lines of evidence suggest that this type of data can be misleading if used in isolation. The correspondence between the homology of genes and that of structures is not simple, and conclusions can be derived only after careful examination of all available data. For instance, the MADS‐box gene family is one of the best‐studied families of transcription factors, and it provides several examples of dissociation between genetic and morphological homology. In this regard, we examine the role ofAPETALA3andPISTILLATAhomologs in the development of petaloid organs, a feature thought to have originated multiple times. We also consider the role of members of theAGAMOUSsubfamily in the development of the pistil, a character that originated only once. Additionally, we discuss how serial homology makes gene co‐option a very common phenomenon in plants. In spite of the multiple cases of this type of dissociation, comparative developmental genetics can yield other types of information that help assess homologies. Furthermore, comparative gene expression studies provide useful data for dissecting the origin of morphological innovations and are, therefore, key to understanding character evolution. Finally, we provide some guidelines for the critical examination of comparative gene expression data in the context of studying morphological innovations.