Like many other theropods discovered in the Yixian Formation, a coat

A & E are straight out because of subject-verb agreement. Among B,C,D B & D use incorrect tense leaving with C as the right choice.

First strike: subject-verb agreement - it should be 'which is' because 'fossil skeleton' and 'a coat of filamentous structures' are singular. A, B and D --> wrong
Second strike: Without knowing the meaning of 'theropods', I would still go with C and not E simply because it is more concise and less cumbersome.

+1 for C.Here is the explanation:

(A) a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers.--> Wrong. Here ‘which are’ written after the comma wrongly modifies the skeleton.Hence it is wrong.
(B) the fossil skeleton had been preserved with a coat of filamentous structures, which are commonly recognized as the precursors of feathers.--> The introduction of ‘had been’ is incorrect.
(C) the fossil skeleton was preserved with a coat of filamentous structures commonly recognized as the precursors of feathers--> Correct.
(D) a coat of filamentous structures, which are commonly recognized as the precursors of feathers, had been preserved with the fossil skeleton.--> The introduction of ‘had been’ is incorrect.
(E) a coat of filamentous structures, commonly recognized as the precursors of feathers, was preserved with the fossil skeleton.--> Wrong. Its the other way around. i.e. to say it is not the skeleton that acts as a coat of filamentous structures, rather it is the filamentous structures that provides a coat to the fossil skeleton.

Like many other theropods discovered in the Yixian Formation, a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers.

(A) a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers.

(B) the fossil skeleton had been preserved with a coat of filamentous structures, which are commonly recognized as the precursors of feathers.

(C) the fossil skeleton was preserved with a coat of filamentous structures commonly recognized as the precursors of feathers.

(D) a coat of filamentous structures, which are commonly recognized as the precursors of feathers, had been preserved with the fossil skeleton.

(E) a coat of filamentous structures, commonly recognized as the precursors of feathers, was preserved with the fossil skeleton.

Answer Choice B & D has unauthorized use of had been,C is not correct for altering the meaning of the sentence or simply ambiguous enough.I eliminate answer Choice A for using "which" incorrectly .So the Correct answer is C

(A) a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers.
(B) the fossil skeleton had been preserved with a coat of filamentous structures, which are commonly recognized as the precursors of feathers.
(C) the fossil skeleton was preserved with a coat of filamentous structures commonly recognized as the precursors of feathers. CORRECT
(D) a coat of filamentous structures, which are commonly recognized as the precursors of feathers, had been preserved with the fossil skeleton.
(E) a coat of filamentous structures, commonly recognized as the precursors of feathers, was preserved with the fossil skeleton. Meaning error

Like many other theropods discovered in the Yixian Formation, a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers.

(A) a coat of filamentous structures was preserved with the fossil skeleton, which are commonly recognized as the precursors of feathers. -Incorrect comparison between theropods and a coat of structures
(B) the fossil skeleton had been preserved with a coat of filamentous structures, which are commonly recognized as the precursors of feathers. -usage of past perfect is wrong.
(C) the fossil skeleton was preserved with a coat of filamentous structures commonly recognized as the precursors of feathers. -Correct
(D) a coat of filamentous structures, which are commonly recognized as the precursors of feathers, had been preserved with the fossil skeleton. -Incorrect comparison between theropods and a coat of structures; usage of past perfect if wrong.
(E) a coat of filamentous structures, commonly recognized as the precursors of feathers, was preserved with the fossil skeleton. -Incorrect comparison between theropods and a coat of structures

A, D and E are straight out. All three compare ‘theropods’ to ‘a coat of filamentous structures’ when it should be compared to ‘the fossil skeleton’. In B the tense is changed, which breaks // ism.

So by PoE, the answer is C.

A, D and E are out - the coat preserved the skeletons, not the other way around. You don't need to be a scientist to understand that skeletons are at the base.

B - SV Agreement issues - "a coat.." is singular, but "which are" = plural

C is correct.

Can anyone help me with why in option B "...had been..." is wrong?