Genes…
Genes are the fabric of individuality. They define every fiber of a pony’s identity; it is through genes that no two ponies are exactly similar, even twins have different DNA sequences. Every creature in Equestria is subject to the harsh realities that their child may possibly be born with a deadly recessive trait in their alleles that could easily kill them at any given time. But it’s not all bad.
Everypony in Equestria shares one trait, the recessive trait of an alicorn. Only 0.02% of Equestria’s population carries its dominant counterpart. And even then there is only a 0.25% chance at giving birth to an alicorn. So needless to say, alicorns are extremely rare. The chances of a stallion and a mare with said complementary gene traits is approximately 0.005%.
In a time long before Luna and Celestia, a time before Canterlot, before Ponyville, before Fillydelphia, there were three separate tribes. Those tribes were, the Pegasi, Earth ponies and the Unicorns, and each cooperated and tolerated each other, but no more than that. The land was consumed with winter storms that never ceased, caused by Windigoes, who fed off of hate, greed and conflict.
Each tribe knew of a land far away from their own, a land free of the tormenting winters of the Windigoes, so naturally each wanted this land for themselves, for different reasons. So to ensure their survival, each tribe sent two emissaries to scout these new and unexplored territories. However, much to their dismay, along with the new land, they also found the same tribes they had tried to escape. The six emissaries began to show signs of conflict in this new land.
However, soon after, blizzards formed once again in this new land, forcing the six into a cave to seek shelter. They came together and huddled for warmth, and reconciled their differences. Soon enough, strong bonds of friendship developed among the six. The storm vanished, and the ice and snow melted, giving way to the new land once more. The six came to terms that they need each other to survive, and formed the united nation of Equestria, bringing their people there to share the message of peace.
The new land of Equestria would be ruled by one pony from each race chosen by their people, to serve on the Cabinet. The Cabinet ruled Equestria fairly and equally as possible, from their new capital city of Canterlot.
About five hundred years after the foundation of Equestria, against near impossible odds, two alicorns would be born. One in Manehattan, when it was still no more than a gathering of shacks towards the far east reaches of Equestria, and the other 20 years later in the southern region of Equestria, just outside of Hoofington.