Sentence Correction

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, 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

[spoiler]Imo D
OA- E(with but?)[/spoiler]

Trenches is plural. It requires yield and not yields .
"arose simultaneously with but independently from" is correct. It suggests that the trenches arose along with city-states of southern Mesopotamia but arose independently from them.

D would be

Trenches yields strong evidence

while E would be

Trenches have yielded strong evidence

Hence E.