is common ancestry that permits him to say something more—that the reason a trait initially evolved actually differs from the reason the trait is now useful.
For Darwinians, a lineage is like a mineshaft that extends from the surface to deep in the earth, with multiple portholes connecting surface to shaft at varying depths. By peering into these portholes, we obtain fallible guidance about what is happening in the shaft; the more portholes there are, the more evidence we can obtain. Common ancestry is not an unrelated add-on that supplements Darwin’s hypothesis of natural selection; rather, common ancestry provides a framework within which hypotheses about natural selection can be tested. It is because of common ancestry that facts about the history of natural selection become knowable.
Tree-thinking is central to reasoning about natural selection, both for Darwin and for modern biology (O’Hara, 1998; Baum and Offner, 2008). The reverse dependence is not part of the Darwinian framework, as we learn from Darwin’s Principle. You do not need to assume that natural selection has been at work to argue for common ancestry; in fact, what Darwin thinks you need to defend hypotheses of common ancestry are traits whose presence cannot be attributed to natural selection. This is the evidential asymmetry that separates common ancestry from natural selection in his theory. So, did Darwin write the Origin backwards? The book is in the right causal order; but evidentially, it is backwards.
I thank Jason Alexander, Francisco Ayala, David Baum, Luc Bovens, James Crow, Daniel Dennett, Marc Ereshefsky, Joshua Filler, Jonathan Hodge, Ronald Numbers, Robert Richards, Michael Ruse, Silvan Schweber, and Mark Taylor for useful discussion.