The first trenches that were cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence for centrally administered complex societies in northern regions of the Middle East that were arising simultaneously with but independently of the more celebrated city-states of southern Mesopotamia, in what is now southern Iraq.
A. that were cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence for centrally administered complex societies in northern regions of the Middle East that were arising simultaneously with but
B. that were cut into a 500-acre site at Tell Hamoukar, Syria, yields strong evidence that centrally administered complex societies in northern regions of the Middle East were arising simultaneously with but also
C. having been cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence that centrally administered complex societies in northern regions of the Middle East were arising simultaneously but
D. cut into a 500-acre site at Tell Hamoukar, Syria, yields strong evidence of centrally administered complex societies in northern regions of the Middle East arising simultaneously but also
E. cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence that centrally administered complex societies in northern regions of the Middle East arose simultaneously with but

答案E，我想问下D怎么错了，为什么这里要用完成时？还有evidence后面的介词结构和从句结构有什么区别吗？

还有D中的but also 是不是前面没有not出现时候，单独出现but also就一定错？

句子主干： trenches have yielded evidence that..........that后面是对evidence的说明，这样就只能在C,E里选了，然后我就不知道再怎么分析了， 根据个人经验having基本都错，所以糊里糊涂选了E。

望赐教！