In reading the flawed original version you get the sense that the sentence is about matriarchal clans, the members of which traced their descent from a common female ancestor.

Then the answer choices can be assessed via effectiveness of conveying that meaning and to a lesser degree by looking at grammar or usage.

(A) This choice sounds right in a way, but really clans of which members is a twisted virtually meaningless expression. The meaning, they are clans made up of which members, is the closest I can come to squeezing some bizarre meaning out of it.

(B) The GMAT prefers that with not be used unless something is actually with something else. This use of with is fairly blatantly suboptimal. So even though maybe in some colloquial sense this version conveys the correct meaning, probably on the GMAT this is not the right answer.

(C) This is easy to eliminate because the pronoun whom is used to refer to people and clans, while made up of people, are not people.

(D) This version effectively conveys the intended meaning.

(E) The clans are not really clans of members. They are clans of people, the members of which ...

So the clear winner is D.