Homology and homocracy revisited: gene expression patterns and hypotheses of homology.

Homocracy, a term referring to shared regulatory gene expression patterns between organs in different animals, was introduced recently in order to prevent inappropriate inference of organ homology based on gene expression data. Non-homologous structures expressing homologous genes, and homologous structures expressing non-homologous genes illustrate that gene expression data is not sufficient on its own to identify morphological homology. However, gene expression data might be useful in testing hypotheses of organ homology, because parsimony can be applied on changes in the relation between expression of orthologous regulatory genes and the formation of homologous organs. A method of testing organ homology hypotheses with respect to change in regulatory gene expression required within a particular phylogenetic context is presented.