Phenotype predictions and evidence.

We made four predictions regarding the phenotypic consequences of the cis-regulatory evolution of the GO “Biological Process” and “Cellular Component” gene sets in Table 1 (we could not make any predictions for “Molecular Function” gene sets). In three cases, confirmation was from previous studies of B6 and CAST, and in one case was demonstrated by us. The up- or down-regulation refers to the branch in which the majority of phenotypic divergence likely took place.