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This is MGMAT CAT Test Question. As per the SC strategy guide regarding usage of pronoun rules the pronoun never refers to nearest noun. However in this sentence the pronoun 'its' refers to super colony . As per the rule it should refer to Ant.
There is NOT a rule that says a pronoun should or should not refer to the closest noun. It has to refer to the correct, unambiguous noun. Often, it's the main subject in the sentence. In the original sentence, its correctly refers to the super-colony.