Darwin ends Chapter 2 with a section entitled Summary, but here he introduces a new, important idea. Yes, he summarizes what he has been discussing, but he provides a new, powerful interpretation:
In genera having more than the average number of species in any country, the species of these genera have more than the average number of varieties. In large genera the species are apt to be closely, but unequally, allied together, forming little clusters round other species. Species very closely allied to other species apparently have restricted ranges. In all these respects the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.
Earlier in the chapter Darwin had made a few comments in passing about creationism, but nothing too significant. But here Darwin introduces the reader to the power behind his long argument. The pattern will repeat many times: long tedious passages followed by the powerful conclusion that nature's evidence falsifies divine creation.
Don't worry if you don't completely follow the observations Darwin discusses in the above quote. Here's what you need to understand. The take home message for evolutionists is that, as usual, there are no viable explanations other than evolution's. The observations may not be fully understood under evolution, but under creation or design the story becomes downright impossible. As Ernst Mayr wrote:
The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.
Indeed, but the default of those opposing theories is not a scientific conclusion. It was evolutionary metaphysics that dictated the outcome. This is the take home message for everyone else. Darwin's reasoning, such as in the passage above, is metaphysical.
The idea that the patterns Darwin was discussing are "utterly inexplicable if species are independent creations" is not from science. Nor did it come from creationists of the day. Nor was it merely a casual observation, made in passing. Then and today, these are the arguments that make evolution a fact. There is no proof that evolution is a fact that does not entail metaphysics. As Stephen Jay Gould observed:
Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.
Religion drives science, and it matters.