One basic piece of evidence for evolution is the the nested hierarchical organization of all organisms, in the form of the "tree of life" or "phylogenetic tree." Page 8 of WEIT has a wonderful diagram of this, listing the characteristics common to each level of the hierarchy. Primates have opposable thumbs, primates and other placental mammals have a placenta, placental mammals and other mammals have hair, mammals and other amniotes (birds and reptiles) have an amniotic egg, amniotes and other vertebrates have vertebrae, and so on. Below is a similar sort of abbreviated phylogenetic tree, though their common features aren't listed.
If God created all of these creatures, he could have made them with any set of characteristics he wanted: fish with placentas, reptiles with opposable thumbs, et cetera. But that's not what we see (and in fact, finding creatures like these would falsify evolution). Instead we find nested hierarchies of characteristics, exactly as we would expect if a common ancestor underwent gradual speciation.
Some creationists try to claim that the hierarchical structure is subjective (which shows it's a problem for them; otherwise they wouldn't object). In Figure 3 of the linked article, Woodmorappe tries to show that wheeled vehicles can form hierarchies, but he can only fit them this way though selective use of data. What about covered wagons, which were much like cars, but with no motor, windshield, horn or thick rubber tires? Many other wheeled vehicles break his delicately constructed mold: tricycles, trains, skateboards, conference bikes and monowheels, to name a few.
Coyne demolishes the claim of subjectivity in the phylogenetic tree with the fact that multiple scientists in the 1700s independently came up with nearly identical organizations. Not only that, but the tree of life established so long ago has been confirmed more recently using DNA evidence. This demonstrates the power of science: multiple sources provide independent confirmation of nested hierarchies and common descent.