We recently saw a dip in natural SE by more than 50% and lot of pages of our have been removed from the index or lost ranking. We have a high reputation and do not indulge in any black hat techniques.
The reason for the same is still unidentified. We are looking for a person who can assist us in identifying and correcting the site again. To our knowledge it is the layout penalty we had. We stated showing an above the fold ad and in a week this all happened. We did not got any policy violation notification as well in the webmaster tools.