For Baragwanathia to appear in the cube, not only does its ancestor, Callunia, needs to be around but Cyclomedusa must be as well. The cubes tempeture needs to be failry high and, as this is the first land organism the player will birth, needs at least some moisture and of course some area of land. The range it fairly large, so it should not be a major concern. After a bit of time with these conditions or by using a Seed of Evolution on Callunia, Baragwanathia should appear.
During the story mode, it becomes available during the first episode: The Cube is born.