I will try to give the explanation the e-GMAT way !!
Sentence structure: Modifier (Verb-ed Modifier) -> Relative(dependent) clause starting with that (Subject - observations, verb - made) -> Comma -> Main Clause (Subject - Darwin and verb -conceived)
Subject and verb agree with each other and we have a subject in underlined as well as non underlined part and this subject makes sense. So, we do not have any subject verb agreement/Subject Verb Must make sense error.
The sentence correctly uses simple past tense, as indicated by the actions made/conceived, for the action that occurred in the past and is a fact. So, we do not have Verb error...
We have a relative pronoun which and this pronoun correctly refers to the noun theory..
We have a modifier starting with 'in which'. Many people have this blind assumption that which SHOULD always be preceded by a comma. But this assumption is not true and fails under circumstances in which a relative pronoun is preceded by a preposition. This indeed is the case over here.. Also note that, we have a modifier exception case over here.. The part 'of natural selection' actually modifies theory and this part can not be placed anywhere else in the sentence without raising the meaning ambiguity..So, it is perfectly alright to say that which correctly refers to theory. Note here that which starts a dependent clause and this clause his own subject (theory) and a verb (evolved). The verb is in the correct tense (Simple past tense)
We do not have any parallelism over here. No lists..
We do not have meaning issues as meaning is conveyed appropriately...
We do not have any idiom issues tested...
So, as per this review, the option A seems to be correct. Note that we have got to this conclusion without reviewing the other answer choices..
<As the lady says in e-GMAT> Please review the answer choices before starting the process of elimination.. lol.
Options B and C use present tense for the action that took place in the past. So, B and C are wrong for using simple present tense. B is also wrong for placing the modifier 'over time' at a wrong place...This modifier should be present after the verb evolve..C too repeats this mistake...
D is wrong for using present perfect tense for the action that took place in the past. Use Present perfect for action that started in the past and continues into the present or whose effect continues into the present...
E is wrong for using whereby...
We have a classic case of joining two independent clauses by merely using a comma...
Two clauses...Charles...selection, whereby all species evolve/have evolved/evolved....
We can use comma to join two clauses only when a comma is followed by a FANBOYS conjunctions and whereby is surely not one of them...So, C, D, AND E are wrong...
Please notice that how understanding the meaning and understanding the sentence parts allowed you to eliminate the wrong answer choices with confidence. So, in a SC question, always make sure that you focus on the meaning and understand the meaning.
Now only the last line is from me: The last line above is the biggest takeaway of mine from e-GMAT..
BTW...I hope I got the answer right coz if I have not, then my entire efforts of writing this explanation will go waste !!

But I think I got this one right....