Let's start by thinking about what we want the sentence to mean. We want the beginning of the sentence ("All Y chromosomes in existence today are descended from") to refer to the Y chromosome of an ancestor, but we want the end of the sentence ("who is thought to have lived about 140,000 years ago") to refer to the ancestor himself.
Because of this, we can start by ruling out A and B, since "who" refers to "a single ancestor's [chromosome]", not "a single ancestor": these sentences basically say "All Y chromosomes in existence today are descended from a single ancestor's [chromosome]. [The single ancestor's chromosome] is thought to have lived about 140,000 years ago." Chromosomes don't live, and we definitely shouldn't refer to them with "who".
We can rule out C for similar reasons: it tells us that all current Y chromosomes are descended from an ancestor, NOT an ancestor's Y chromosome. People descend from people, while chromosomes descend from chromosomes. So this answer choice doesn't make much sense.
D and E both solve the problem with the phrase "the Y chromosome of a single ancestor", which allows the first part of the sentence to refer to "Y chromosome of a single ancestor", while the last part of the sentence refers to only "a single ancestor".
To decide between D and E, we should identify their two primary differences: "who" vs. "whom" and "is thought/have lived" vs. "was thought/had lived". If we look at the first sentence, we see that the intended meaning of the sentence is that we *currently* think that the ancestor lived 140,000 years ago. There is nothing to indicated that we *used to think* the ancestor lived 140,000 years ago, but we now think something different. So we can eliminate E and pick D. (Note: we can eliminate B for the same incorrect use of past tense.)
We can also use "who" vs. "whom" to eliminate. "Who" should be used when it refers to a subject, while "whom" should be used when it refers to an object. A quick and easy rule of thumb is that we should be able to replace "who" with "he/she/they" and "whom" with "him/her/them". This gives us:
D. All Y chromosomes in existence today are descended from the Y chromosome of a single ancestor. He is thought to have lived about 140,000 years ago.
E. All Y chromosomes in existence today are descended from the Y chromosome of a single ancestor. Him it was thought had lived about 140,000 years ago.
This makes it clear that D is the correct option. (Note: we can eliminate C for the same incorrect usage of "whom".)
Hope this helps!
