If there are they shouldn't.

As mickeyben says above, choosing indexes is a compromise - you sacrifice performance in one area for performance in another. Only you can make the right decision there, because only you can begin to know how the app will be used in production.

DataMapper's dm-constraints plugin (https://github.com/datamapper/dm-constraints) can automatically add foreign key constraints to your associations, which has the side effect (in MySQL at least) of creating indices on the foreign key columns if they don't already exist.