Gene regulation in whale development
In the whale study, as with this slightly older study of bat development, the massive changes between the ancestral species and the highly derived modern species are readily visible and appear massive. One might easily ask how such massive changes could happen. What was added to produce the bat's wing? What went away that made the whale's legs disappear? Decades ago, even if we had fossils to demonstrate that such transitions had in fact taken place, we had no idea how a shrewlike ancestor could have turned into whale or a bat.
It turns out that those questions which seemed quite reasonable not long ago were built on faulty premises. Small changes in gene expression, not the addition or deletion of genes themselves, are sufficient to produce dramatic changes in the adult morphology. What seem like unbridgeable gaps between modern whales or modern bats and the ancestral mammal turn out to be very small gaps when you make the changes at the right stage in development.
If you haven't read Endless Forms Most Beautiful: The New Science of Evo Devo by Sean B. Carroll, you really should. This is a new field in biology, and it's opening up amazing new opportunities.