These homologies between vertebrates have been known about for many years. The middle ear bone homologies were figured out by Reichart in 1837, years before either Darwin or Haeckel. There is no room here to explain the extraordinary similarities in the developing pharynx of all vertebrates, but I will refer to Troy Brittain’s blog on this, which is a truly magnificent piece of work (and tackles many of the creationist misrepresentations).