For Baragwanathia to appear in the cube, not only does its ancestor, Callunia, need to be around but Cyclomedusa must be as well. The cube's temperature needs to be fairly 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 is 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.
In story mode, it becomes available during the first episode: The Cube is born.
Although it is the first land plant you get in the game, it wasn't the first land plant in real life. That title goes to Cooksonia, which doesn't appear in the game