All Y-chromosomes in existence today are descended from

let us analyze each of the answer options -

A - "a single ancestor's" what? this answer option does not answer the question.

B - "a single ancestor's" what?

the "who" refers to "ancestor's". It should have referred to ancestor.
Also, we need the present tense here - 'who was thought to live'; the "thinking" is still true. so, the subordinate clause should read - "who is thought to have lived".

C - it makes more sense to say that the chromosomes today descended from another chromosome.
We need to use "who" not "whom"; Whom is used to refer to objects whereas who refers to subjects.

For example -
Who likes some pizza? (He does)
Whom do you believe? (I cannot say "he"; I say - I believe him).

the usage of "it" is incorrect as it does not refer to anything.
Also, the usage of past perfect is incorrect. We are referring to a specific time - 140,000 years ago. We use the past tense in such cases.

D - correct answer.
Note the sequence of tenses used here -
"who is thought to have lived 140,000 years ago" - the thinking is in the present.
to + past participle suggests that the action occurred before the preceding verb. Hence, this correctly suggests that "living" occurred before "thinking".

E - "whom it was thought had lived"

the usage of whom is incorrect.
Also, the present tense "is thought" is better here.