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You need "that" to connect the sentence, so (D) is out.
"but" in (C) changes the meaning of sentence, as we need to have sense of continuty here(Universe started ..... and has [over the period of time] metamorphesed into .......)
This sense is clear only in (B) and (E) ((A) having begun is wrong) i think in first sentence we need simple past tense to make the relation.
Between (B) and (E), (Again in (E) i think we need simple past) so (B) is best IMO.
Check out this awesome article about Anderson on Poets Quants, http://poetsandquants.com/2015/01/02/uclas-anderson-school-morphs-into-a-friendly-tech-hub/ . Anderson is a great place! Sorry for the lack of updates recently. I...