First off, I will be referencing future episodes in my supporting material.
Theory 1: Project Eureka and Project Anemone were two names given to a line of research that has been underway ever since Eureka was discovered.
My supporting material for this is the linch pin of the whole idea.
Now why do I think Project Eureka and Project Anemone were connected?
There are only three images of Eureka from the time prior to being connected to Project Archetype.
This is Eureka with her caretakers/handlers on the first day she attempted to pilot the Type Zero.

Notice the clothes worn by Misha and the three figures behind Eureka.
Next we move to a scene from the Novak Foundation. This is the caretakers/handlers for the 3 possible replacements for Anemone that Dominic went to Warusawa to meet.

Here's another shot. I'm not sure who the man in the lab jacket is but I believe he fills the same position Misha did with Eureka.

Here, this is from episode 13. After Dominic and Renton pull Eureka and Anemone out of the Hypocenter of the Coralian Eureka is taken to Gekkostate and Anemone to the Izume. This is the team of scientists that tend to Anemone. Look Familiar?

Here's another shot.

It is certain that these people are the doctors behind the creation of Anemone and responsible for her maintenance. The source of Anemone's mixed DNA must have been Eureka.
I believe that Misha was the one who maintained Eureka for the Novak Foundation. When she defected from the group and ran with Holland the man above was put in her place and the DNA was used to create Anemone.