The tree of harmony. We have almost no cannon about it, leaving it open for ideas to come flying out of my awesomely epic brain. So, without further adieu, is my headcannon.

Simple answer?

Clover the Clever's spell.

The long?

Clover's spell was the first time all three pony races had felt friendship and harmony. Before this point in time, they had been seemingly at war with each other. They realize they're all ponies,blah blah blah, friendship heart,,windegoes defeated. On top of that it was in a cave. The tree, in a cave. You could see where Canterlot would be. You can see Canterlot from Ponyville. But Clover's cave was higher! Erosion. This happened over one thousand years ago, it's going to erode.