I'm not even asking for examples. Just a simple process. I think that a simplistic answer would be that morphology, physiology and to a large extent, behavior are all under genetic control. DNA is subject to alteration by a variety of uncommon events called mutations. These include base substitutions, frameshifts, as well as partial and complete duplications of genes.
Alterations can occur in the controlling mechanisms of genes as well as in the genes themselves.
Mutations can lead to marked changes in metabolic abilities of organisms as well as substantial morphological alterations, and these types of transformations have been well documented. Obviously, most of the studies that have been done in these areas are performed on bacteria for logistical reasons, but a lot of the same mechanisms have been seen in eukaryotes. If you want to present objections to the idea that successive changes in the genome can result in the type of evolutionary events that leave you incredulous, then go ahead. If you want specifics on how each metabolic pathway developed or how a given organ was generated, I would like to see how you would propose to study such matters. A lot of the report is speculation.