There are several differences between the two, but the biggest distinction between them is that eukaryotic cells have a distinct nucleus containing the cell's genetic material, while prokaryotic cells don't have a nucleus and have free-floating genetic material instead.
A scientist may use molecules - enzymes, proteins, DNA, RNA - to test for similarities, because if anatomy alone was used, it would be difficult to link traits and characteristics between the two organisms. For example, a rabbit has an endoskeleton and a closed circulatory system, while a fly has an exoskeleton and hemocoel.
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I think the answer is B but it could also be A