"However, it does not follow that A = E. Were C to be cut out, then there would be two differing "species."
Cut out as in removed from the chain? Or nonexistant?
If it's nonexistant that how would you get from A to E?
If A=B=C=D=E and D were cut out, would that also lead to differing species? Or would the final step not occur?
Cut out, not non-existant. A link may be removed from an existing chain.
Ring species are an example. There are some mountains (I'm not sure where; I saw this about 50 years ago.) where plants can interbreed with their neighbors but not with others of "the same species" on the other side.