Fig. 1.

Evolutionary scenario that would give rise to inconsistent orthology relationships for different domains in a protein. The hypothetical red and blue domains are evolving by descent along the species tree of the species X, M and H, giving rise to extant proteins X1, M1, H1, H2, M2 and X2. After a duplication of protein H2 in species H, this blue domain was inserted into red-domain protein H1, such that protein H1 now has two domains. Therefore, H1’s red domain is orthologous to M1 and X1, whereas its blue domain is orthologous to M2 and X2