The use of phylogenetic testing in the study of gene expression patterns and to infer ancestral developmental roles. A mixture of orthologous and paralogous genes is included in this phylogenetic tree, therefore reflecting gene relationships rather than relationships of taxa. The phylogeny of taxa can be inferred by analyzing either set of orthologous genes. The two lineages (A and B) of orthologous gene copies are shown in capital letters, and the B lineage is additionally highlighted in grey, while recent paralogues are numbered. Triangles, squares and hexagons indicate gene expression in three tissues/organs, which are grouped by superficial similarity as primary homology hypothesis. Homocratic structures are defined by co-expression of identical patterning genes, but these can be either orthologues or paralogues. In the latter case they do not strengthen a homology hypothesis because convergent evolution is likely (as in the depicted case).