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"I wish to thank an anonymous referee for PPQ for his suggestions which helped to improve the presentation of this paper".

This is the way I've usually seen this kind of sentence: without a comma before "which". But do you think it is the only possibility. For what it's worth, in Spanish I'd probably put a comma.

Sextus
+0
I suppose without the comma it might be taken to mean that he'd made other suggestions, which were frankly rubbish, and which you've silently ignored...

You could say "suggestions, which greatly improved...".

MrP
Comments  
Students: We have free audio pronunciation exercises.
Or perhaps: "...for his useful suggestions, which..." Also, in theory a suggestion may help to improve sth, but can it itself improve sth?

Sextus
Yes, I think so; "suggestion" can encompass both the act of suggesting and the suggested action.

MrP