Using trees to make predictions about fossils: The whale's ankle
Scientists used to think that whales' ancestors were now-extinct carnivores called mesonychids. However, based on recent findings, scientists have hypothesized that whales are actually more closely related to hoofed mammals like hippos and ruminants such as cows and giraffes.
This hypothesized phylogeny leads us to predict that ancient whales should share some characters with their close relatives. The close relatives of whales have a type of ankle called a double pulley ankle, so we would expect that ancestral whales would also have a double pulley ankle.
And in fact, recent fossil discoveries have borne out that prediction. Scientists found ancient whales with hind legs and pelvises: these whales had the same kind of double pulley ankle bone that modern pronghorns, camels, cows and hippos have.
Compare the ankle bones of the two ancient whales on the left and right (the specimen on the right is missing some bones) and those of a modern pronghorn (center). Notice the double pulley structure boxed on all three.