Neither, they used a spell that let them become a stallion temporarily which allowed the other to get pregnant. So they are both the biological parents.
Nebula was born from Trixie and Aurora was born form Twilight, their last names depend on who was "the father" (Therefore Nebula's full name is Nebula Sparkle while Aurora's is Aurora Lulamoon.)
Rainbow and Applejack also did this so Rainbow would get pregnant with little Nimbus. Everyone else so far has been a mare and stallion pairing. (Except for Rarity and Spike since Spike is a dragon.) Currently Pinkie's pregnant right now.
Makes you wonder what the Sparity kid will look like. I've seen pretty interesting Kirins. But then we have to remember in one of the earlier posts Spike's mind tells us her read something saying "Its not known if dragons and ponies can reproduce." Could make an interesting story under the right conditions.