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During the events of Assassin's Creed, Desmond can read Vidic's E-mails. They confirm that Abstergo are in possession of all of the Mitchell-Hedges Crystal Skulls, which allow them to communicate over long distances without any fear of Assassins eavesdropping. That is the most recent time they have come up in the series. They are not listed as Pieces of Eden. The legend tells of THIRTEEN skulls. There a thirteen (including one "retired") Gods and goddesses in Roman/Greek mythology, so presumably thirteen of Those Who Came Before (as all "god-figures" in religion are primitive representations of them). I think it's very possible that the skulls are the remains of TWCB. If this is true, it may be possible that they are the skulls of the ancient race.
It may also be possible that the Templars are aware of this, as NASA is a Templar organisation and it named it's moon missions: "Apollo"