The nomadic ponies traveled far and wide across the land that would eventually be Equestria, moving with the food. Pegasi tended to follow the migratory patterns of large birds, unicorns the movements of prey herds, and earth ponies the same vegetation that the prey herds were tracking. Eventually, the earth ponies would reach the rich foothills of the Crystal Mountains, where runoff from the icy peaks met fertile soil in a wonderful climate for agriculture.
While the unicorns moved on, the earth ponies lingered for some time, using seeds from the local plants as well as those they had collected on their journeys to begin experimenting with agriculture. They felled the sparse forests to create permanent homes and settled into the first civilization of ponies. They became almost wholly herbivorous in diet, with meat becoming a rare treat enjoyed as wildlife came and went with the seasons, and the still-nomadic pegasi and unicorns appeared with extra meat rations and disappeared with more stable plant-based foods.
Unicorns were the first to join the earth ponies in settling the Crystal Mountain foothills. Game had become harder to track, and the unicorns were ultimately losing out to better pegasus hunters. They were less capable of agricultural exploits than the earth ponies, but managed to trade food for better tools and magical assistance. They also lent themselves well to administrative capabilities, and helped to manage planning and crop rotations.
Pegasi soon began to settle as well, mostly because of the strain the long migratory flights put on them. They had already begun showing signs of weather manipulation capability, but it had little use given the natural healthy inflow of water to the hills, and they mostly operated as scouts, guards and hunters. They were the last of the three races to adopt herbivorism as their main diet.
It is at this point that the specific callings we now know as cutie marks began to come together, though the marks themselves would not appear immediately. However, ponies were able to focus on more specific tasks after settling down, with families of earth ponies becoming experts in particular plants, artisans becoming experts in the creation of certain tools, and pegasi focusing on mastering particular weapons.