Beg Pardon? His theory was based on his observations while on the Beagle, and he assumed that the changes her observed were based on enviromental factors. I agree that he was studying populations,and the very title is misleading, but once one gets beyond what he actually said and into the uses made of his conclusions, natural selection was treated as a cause by his followers. He himself was caught up in this. His book the Descent of Man, is based on what? Wholly speculative.
Descent of mans speculations paid off in spades with fossils of Australopithecus and molecular genetic data. The evidence of our common ancestry is right down to the molecular level.