We unfortunately have very little documentation on ponies prior to the creation of the Three Great Tribes, as there is no historical record and a very limited fossil record. However, what we do have is enough to at least make an educated guess as to the origins of our species.
The oldest pony remains have been found much where modern ponies are now: the plains around Canterlot Mountain. Of course, the mountain itself was hardly what it is today, as at the time the Saddle and Crystal landmasses had just started to meet (just being relative, of course, as the two were already beginning to buckle together), and it would be many thousands of years before the peaks would reach their great heights.
Ponies back then were quite different from the creatures they are today. Scientists suggest that the coats of our ancestors were much duller in color, taking shades more apt to their environment as camouflage. However, a much larger difference was in the apparent diet of prehistoric ponies. They were predators, and while the grains, fruits, flowers, and grasses that make up our diet today were certainly part of their food stock at the time, they were also apt to eat other animals, and it is thought that they were vicious hunters. Despite their vast differences, though, they also had many of the key traits that would remain in the pony bloodline even today.
Prehistoric earth ponies were the first of the subspecies to exist, and their usual tactic was one of endurance. They could pursue their prey for great distances, simply outlasting the animals' abilities to run while feeding off of wild plants in the meantime. In the case they had to defend themselves, their great bulk and fortitude came into play. They could survive wounds that would cripple other animals, and their large herds allowed them strength in numbers.
It's unclear whether pegasi emerged before unicorns, but it is known that the growth of the earth pony population made hunting ground game a much harder issue. The pegasi's wings were definitely a strange development, and one that's extremely hard to trace, much less understand, to the point where a hypothesis has caught on that they were an entirely different species, possibly related to the griffins, that somehow merged into the pony bloodline. Whatever the case, their wings were a great boon, allowing them to hunt aerial prey and to scout for ground prey much farther than their earth-bound brethren. They sacrificed the bulk and endurance of the earth ponies, but gained a new resilience as they learned to fling themselves on ground prey in great dives, breaking the target's bones with crushing force without harming themselves. It is unknown whether these proto-pegasi were able to manipulate clouds and weather as they can now, and whether it was ever used for any purpose at this point.
Unicorns, unlike pegasi, were definitely a development of earth ponies, in response to the magical nature of the world. It is a long-held theory that magic is a fundament of the universe, rather than a biological development, and magical creatures are simply ones that learned to tap into this power. Unicorns gained a horn atop their heads, likely at first a mere focus for magical energy unlike the complex extension of the brain prevailing today, allowing them to point magic at far away objects to manipulate them. It was likely rather rudimentary, but it could still be used as a weapon, whether to trip up pursued prey or to deal them direct physical harm.
The three races were perhaps not terribly close, but they still mingled enough to provide the interbreeding needed to keep them as a single species. This interbreeding likely helped to generate the variety of colors that our race sees today, as well, as the different races would have had different camouflages in order to blend in to their different surroundings better, from the blue of the skies to the green of grasses to the many colors of the earth.