The ancient Anasazi harvested such native desert vegetation as the purple-flowered bee plant, what they now commonly call wild spinach in northern Arizona and other parts of the southwestern United States.

A) what they now commonly call

B) a plant that they now commonly call

C) now commonly called

D) and is now commonly called

E) which it is now commonly called

Two propositions are grammatically and semantically correct:

C) now commonly called E) which is now commonly called

We are told in the sentence that the purple-flowered bee plant is called wild spinach in what we can assume to be today's Arizona and other parts of the Southwest. This comes as opposed to the context of the beginning of the sentence, which evokes the past, as evidenced by the adjective "ancient."

Therefore, it makes sense to clarify that the plant's new common name is not what the ancient Anasazi used to call it, but what modern-day Americans use. This is why the subject of this clause should be the plant itself ("which") and not the Anasazi.