I was matching the plurality to singular "mechanism". That is, I was intending to use #1 of the following:
"Fruits are an evolutionary mechanism, which is ..."
"Fruits are an evolutionary mechanism, which are ..."
What is the correct way of phrasing this sentence, and why?
ANSWER: You should probably phrase it the way you had originally intended, which is with version #1 with "is" since you had intended to use the prior nominal "evolutionary mechanism" of the main clause to be the antecedent of the relative word "which".
Your example seems to involve a supplementary relative clause. In your example, the relative element is the subject in the relative clause. And so, in general, the number of the tensed verb in the relative clause will be the same as the number of its antecedent. That is:
- If the antecedent is plural (e.g. a plural noun), then the relative clause will usually use a plural verb; and if the antecedent is singular (e.g. a singular noun or a clause), then the relative clause will usually use a singular verb.
In your specific case, you intended to use the main clause's "evolutionary mechanism" as the antecedent for the relative "which", and so, the relative clause's tensed verb should be "is" -- which is what you had intended to do all along.
[CAVEAT: This answer post is working on the assumption that your question involves determining the number of the tensed verb ("is" versus "are") in the supplementary relative clause. And so, I'm assuming that the ellipsis in your example is representing the rest of that relative clause.]
TOPIC: integrated versus supplementary relative clause
Along one dimension, there are two main types of relative clause:
integrated relative clause:
Traditional grammar uses the term "restrictive" (instead of "integrated"), but their terminology is misleading because many "restrictive" relative clauses are not restrictive in their usage.
An integrated relative clause is often, or usually, integrated into the noun phrase (NP) that contains the relative's antecedent, e.g. "The boy [who had shot the dog]". Sometimes the relative clause has been raised up into clause structure so that it is no longer part of the NP that contains the relative's antecedent, e.g. "A stranger came into the room [who looked just like Uncle Oswald]" (CGEL page 1066, [22.i]).
supplementary relative clause:
Traditional grammar uses the term "nonrestrictive" (instead of "supplementary"), but their terminology is misleading.
A supplementary relative clause is not integrated into the noun phrase (NP) that contains the relative's antecedent, nor is it integrated into the clause structure that contains the relative's antecedent. It is detached from the main clause, which is usually done by punctuation.
The rest of this answer post will deal with the supplementary relative clause, since that is the type that's involved in the OP's example.
TOPIC: clause as an antecedent for the supplementary relative clause
The supplementary relative clause can have many different types of antecedent. One type that the supplementary relative can have as antecedent but the integrated relative cannot is that of clause.
CGEL page 1060:
Only supplementary relatives can have a clause as antecedent:
 He said he'd drafted the report, [which I knew to be untrue]. -- (supplementary)
The antecedent of which is the clause he'd drafted the report; the relative clause in such cases can only be of the supplementary type, with a separate intonation contour.
A supplementary relative can also have a nominal as its antecedent (a nominal is usually the antecedent for an integrated relative).
And so, for your specific example, the supplementary relative could have as its antecedent one of three possible candidates:
the clause: "Fruits are an evolutionary mechanism"
the nominal: "Fruits"
the nominal: "evolutionary mechanism"
CONCLUSION: It depends on what is in the rest of the supplementary relative clause of your example and on the intention of the writer, as to whether the number of the relative's head verb is singular or plural ("is" versus "are").
NOTE: CGEL is the 2002 reference grammar by Huddleston and Pullum (et al.), The Cambridge Grammar of the English Language.