Choice D is the best answer. The subject is the compound noun phrase "Kyoto and its surrounding areas." No punctuation should separate the parts of a compound subject, nor should punctuation separate the subject from the verb "have."

Choice A is incorrect because the commas separate the subject parts and the subject from the verb. Choice B is incorrect because the dash acts as an interrupter that isn't closed. Choice C is incorrect because the comma after "Kyoto" disrupts the compound subject.