"It was evident that such facts as these, as well as many others, could only be explained on the supposition that species gradually become modified; and the subject haunted me. But it was equally evident that neither the action of the surrounding conditions, nor the will of the organism (especially in the case of plants) could account for the innumerable cases in which organisms of every kind are beautifully adapted to their habits of life - for instance, a woodpecker or a tree-frog to climb trees, or a seed for dispersal by hooks or plumes. I had always been much struck by such adaptations, and until these could be explained it seemed to me almost useless to endeavour to prove by indirect evidence that species have been modified." Charles Darwin, Autobiography
My translation: species have changed their body forms (phenotype) through time. It wasn't the environment affecting them directly and it wasn't them wanting to change (Lamarck) so it must be something else.