The transformation seems to have coincided with the origin of digits and tetrapod pelvis, at the internode traditionally taken to mark the 'origin of tetrapods. What they are saying is that the development of the braincase is developmentally linked to the limbs. A recent study in Nature showed that most of the change between a flower that looked designed to attract hummingbirds and one that looked to be designed for bumblebees was accomplished by 8 mutations and that is all. We are on the verge of an age of experimental evolution to retrace which mutations separate species. In the case of monkey flowers, it was only 8 mutations.
Darwinian selection is still operative.