So what was with that title, Origin of Species, then?
A typical quote from Origin of Species:
I can answer these questions and objections only on the supposition that the geological record is far more imperfect than most geologists believe...That the geologic record is imperfect all will admit; but that it is imperfect to the degree required by our theory, few will be inclined to admit.
You'll find a number of similar quotes at the link.
"Darwin's early scientific experience was primarily as a geologist, and much of what he had to say about the nature of the fossil record (summarized in the passage quoted above) was an accurate and insightful early contribution to our understanding of the vagaries of deposition and the preservation of fossils. But his Chapter 9 (first edition) on the imperfections of the geological record is one long ad hoc, special-pleading argument designed to rationalize, to flat-out explain away, the differences between what he saw as logical predictions derived from his theory and the facts of the fossil record." (Eldredge, Niles [Chairman and Curator of Invertebrates, American Museum of Natural History], "Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria", Simon & Schuster: New York NY, 1985, pp.27-28.)
Darwin studied trans-mutations in various animal species under certain enviromental conditions and then Hypothesised that on a longer time scale that animals and (possibly humans) would eventually mutate into a completely other species. That why its still called the “THEORY” of evolution.