When asked her opinion on the discovery of the remains of an ancient civilization, Derpy Hooves, the accidental discoverer of the ruins, said this:
"Well, when I saw the pictures on the walls, like the one on this table over here, I thought, 'Gee, I wonder why those Ponies are letting those monkeys sit on them like that?' So I told miss Twilight Sparkle about this and she said, 'According to my research, there was once an ancient race of apes known as the Humans. They enslaved our ancestors, the Horses, and used them for transportation, labor, and for companionship.' I decided that I do not like humans after hearing that."
Well... It stands to reason given various similarities between Human and Equestrian culture. And due to the apparent sharing of constellations by both worlds, it further stands to reason that they would either be located very close together in the galaxy or be one and the same. I suggest an analysis of known Equestrian constellations for differences. Unfortunately, I can only think of one constellation specifically show in MLP, and that was Canis Major, and it looked identical.
Furthermore, there is always the possibility that the planets are one and the same, perhaps separated by a dimensional barrier that allows humans to influence ponies unintentionally through some unknown empathic link.
The final possibility, and most likely, is that some catastrophe in the future forces Humanity to abandon the Earth or to die off. Most likely the former. As a result, genetically bred horses gradually developed sentience and you know the rest.
However, from all this, I am forced to conclude that I think about these things way to much.
As you can clearly see, our ancestors interacted and even served under the beings known as humans. Our ancestors were of a larger size, in order for the humans to ride them. That explains the origin of the saddle, which is a remnant of our ancestor's early history, which we use for fashion and clothing today. Therefore we can only conclude one thing: HUMANS