Changes to main Database during Transactional Replication
By default, replication will push out the following DDL changes to subscribers:


ALTER TABLE
ALTER VIEW
ALTER PROCEDURE
ALTER FUNCTION
ALTER TRIGGER


And by default, I mean unless you have specified otherwise when you made a call to sp_addpublication when setting up the publication (even if done through the GUI, this is the underlying stored procedure that is called).  There is a parameter for that stored procedure, @replicate_ddl, that is set to 1 by default, meaning that the above DDL commands will replicate to subscribers for the articles in the publication.

When you made your initial call to sp_addarticle, you would have specified (again, even if through the GUI where all the article options are set) which indexes (clustered and nonclustered) were generated for subscribers to create for initialization as well.

Reference :: How to: Replicate Schema Changes