My Year of Darwin: 7/12/2014 What initially led Darwin to propose descent with modification

"I had been deeply impressed by discovering in the Pampean formation great fossil animals covered with armour like than on the existing armadillos; secondly, by the manner in which closely allied animals replace one another in proceeding southwards over the Continent; and thirdly, by the South American character of most of the productions of the Galapagos archipelago, and more especially by the manner in which they differ slightly on each island of the group; none of the islands appearing to be very ancient in a geological sense." Charles Darwin, Autobiography

To be explicit, Darwin is proposing that organisms originate from other organisms - the origin of species. This isn't entirely novel and he isn't proposing a mechanism (yet). But he is, quite clearly, rejecting special creation, which was the accepted explanation for the origin of species. 

Brain is fried from getting up at 315. But what a great day in the field.