In this study, we analyze the role of different structural variants of proteins in the speciation processes. We separate human and mouse proteomes (taken as a reference) into three previously defined variants of disorder: ordered proteins (ORDPs), structured proteins with intrinsically disordered protein regions (IDPRs), and intrinsically disordered proteins (IDPs). Then, using the representation we call here Forsdyke plot, we study the correlation of DNA divergence with the corresponding protein (phenotypic) divergence in the three variants, comparing human and mouse coding sequences with their homologs from 26 eukaryotes. The parameters of the correlation are related to the speciation process. We find that the three variants of disordered proteins are differently related to the speciation process. Specifically, IDPs phenotypically diverge earlier than ORDPs and IDPRs. ORDPs diverge later but are phenotypically more reactive to nucleotide mutations than IDPRs and IDPs. Finally, IDPRs appear to diverge phenotypically later than IDPs, like ORDPs, but they are prone to accept mutations with rates that are similar to those of IDPs. We conclude that IDPs are involved in the early stages of the speciation process, whereas mutations in ORDPs, once speciation is initiated, accelerate phenotypic divergence.