I just was reading parts of Origin of Species again for an encyclopedia entry that I am writing. As usual, it's abundantly clear that Charles Darwin was thinking clearly, in this case about tree thinking versus linear thinking. In Chapter 6 (Difficulties on Theory), he clearly distinguishes linear thinking and tree thinking.
"In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition."
Today, we have statistical methods that we use for making inferences about lineal ancestors, which depend on the phylogenetic relationships among the collateral descendants. But, as I've written in other posts, people often confuse collateral descendants with the actual lineal ancestors.