The Genetics of the Pony

This is a mini-project that I did in my free time. Yes it's a long read, but worth it if you enjoy putting science into Ponies!

It's just my idea of how pony types are passed from generation to generation, and the genetic specifics associated with the hereditary nature of pony type.

As a note, the section on the Elements of Harmony at the end has no scientific basis and exists literally as a mere whim of mine, something to make wielding the Elements a prestigious role. It was pointed out by ~Twinflamable that this section is extremely speculative. I have therefore edited the document, completely removing the Elements section from the theory, placing it as a post-conclusion thought.

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EDIT
For anyone wondering about the Season 3 Finale, Magical Mystery Cure, and how it relates to this, here's my theory: there exists magic, which Twilight/Celestia are able to access, that modifies genes. Not exactly possible in standard genetics, but this is FiM, so anything is possible.
(i.e., Twilight was, for instance, [pp NN Aa], and the magic she used changed her to [PP NN aa] or [Pp Nn aa], or perhaps forced the expression of the Pegasus gene even though it was completely recessive)