Homology relationships at different hierarchical levels of biological organization (ge: gene; gn: gene network; gi: gene interactions in the network; e: embryonic origin; m: morphological structure) following the suggestions detailed by Abouheif . (A) Functioning of homologous genes in structures of independent evolutionary origin. In insect and vertebrate eyes, a very similar genetic machinery is used to generate structures that are historically non-homologous and morphologically dissimilar. Note that this generative homology is different from latent homology (B) in that the latter is concerned with morphologically homologous structures. This figure illustrates the difference between two main concepts, historical vs. generative homology. (B) Latent homology or re-awakening. If morphologically homologous characters, such as arthropod compound eyes , have multiple independent origins on a phylogeny then this may be due to retained genetic programmes that are not expressed in some of the ancestors, but whose functionality has been recovered after further speciation, giving the incorrect impression of convergent evolution. (C) Partial homology of gene networks. Novel genes (V, W, X, Y) are recruited into an ancestral network consisting of genes A, B, and C in two different lineages of taxa (a+b and e). Thus, the black part of the network is homologous (inherited from a common ancestor) while the coloured segments are not.