Bunuel
Prompted by observations of seemingly related species in neighboring locales that he made during his five-year voyage around the world on the HMS Beagle, Charles Darwin conceived his theory of natural selection in which all species evolved over time from a single ancestor or very few common ancestors.
A. in which all species evolved over time from a single ancestor or very few common ancestors
B. in which all species evolve from a single ancestor or very few common ancestors over time
C. whereby over time all species evolve from a single ancestor or very few common ancestors
D. whereby all species have evolved over time from a single ancestor or very few common ancestors
E. whereby all species evolved over time from a single ancestor or very few common ancestors
First, prepositional phrase "in which..." modifies the process of natural selection.
In which denotes a place or process in which something occurs.
Whereby basically means "means by which" something occurs.
Natural selection is the process "by which" all species evolve... so it makes sense to use "whereby" instead of "in which". Eliminate A and B.
Second, verb tense "have evolved" over time makes more sense than the simple past tense ("evolved") or "evolve"
Minor issue...and not so sure if this is the right approach but "over time" should modify the verb "evolve"; as such, placing "over time" at the end of sentence (option B) or before the verb (option C) seemed less likely...