A removed message from Eleanor revealed that Delta is her biological father (Sophia picked his DNA randomly from a bunch of archived DNA).
Originally their was only one Big Sister, Eleanor, who couldn't adjust to life on the surface and returned to Rapture. Furthermore, she would have been the one kidnapping children, and making them Little Sisters. However, this was removed as the game designers felt this twist was too predictable. You also would have played as the first Big Daddy, who as a result could think for himself, and could use plasmids as a result.