If I had to guess, I'd say that the unicorn/pegasus/earth pony status is determined by multiple genetic loci, which is a fancy way of saying that it's dependent upon many, many genes. This would pretty much mean that general trends are the best you can do in terms of prediction, and it becomes less accurate to think of traits in terms of simple dominant or recessive character. Kind of like human height or skin/hair color.
To my mind, the most likely explanation for the emergence of the three sub-types is that they were originally one type that split into three separate, fairly isolated populations, and some degree of speciation occurred. Again, kind of like what happened with humans, although with us, the differences are mostly cosmetic, whereas in the case of ponies, they're more functional. Of course, that's assuming that ponies arose through Darwinian evolution, as we did. Given that we don't really know the limits of magic in the show, it's possible that they were created in their current forms by some god-like being, but we haven't really seen anything to suggest that this is the case. Also, the fact that pony heredity seems to follow rules at least decently similar to our own (i.e., they reproduce with variation) means that Darwinian evolution at least applies to them, even if it doesn't necessarily establish it as the only possibility for the initial appearance of the species.
edited 15th Jan '12 1:40:48 PM by Hsere
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