Genetic Hypotheticizing · 10:15pm May 18th, 2016
We have three primary phenotypes (earth pony, pegasus, unicorn). All are interfertile and produce fertile offspring (vide. the Cake family), and the children of parents both of a single phenotype can be of one of the other phenotypes. No intermediate forms are noted (but see below).
There is also the alicorn phenotype (which manifests the traits of all three phenotypes - although these are only particularly visible traits in the case of pegasi and unicorns), which is somewhere between extremely rare and not naturally occurring.
Hypothesis: these are obviously all the same species. The phenotype manifested is controlled by three entire gene-complexes, each controlled by a common activator. Whichever is dominant represses the other two. This repression may or may not be complete; if not complete, it would lead to interesting consequences like this - http://www.fimfiction.net/story/153395/6/the-rites-encyclopedia/pony-genetics-tribe-hybrids - which ideas I may totally swipe for my own use.
Alicorns are therefore the product of a rare mutation that represses the repressors. I would further postulate that this is usually a lethal mutation, and requires a co-mutation to permit stable expression of the multiple traits, which is why they almost never exist without magical intervention.
This hypothesis implies obviously that all three have a common ancestor. Given the wings of the pegasi and what we know about limbs in the evolution of Earth life, it seems likely that this was a common hexapedal ancestor (so, there goes most, albeit not all, chance of non-coincidental relationship to Earth genus Equus), which in turn suggests that it is likely that traces of the unique traits of each phenotype are also found in the other phenotypes in vestigial form, especially where they interact with other parts of the body: if one goes looking at the skeleton of an earth pony or unicorn, one can probably find the modified vertebra where the wings (formerly, possibly, a mid-leg) would hook up to the spine if they were a pegasus; likewise, a vestigial horn root may be found in earth ponies and pegasi. (This also suggests a variety of interestingly horrible potential hereditary birth defects that I'm not going to go into at this time.)
Extending this theory to the other sophont equines is left as an exercise for the reader's wild speculation.
(As is the wild-assed possibility of genetic manipulation and xenosplicing such that Lyra can have hands.)
Equestria's gonna be friends with an empire of star-trotting, immortal, planet-busting hyper-entrepreneurs, who also happen to have the means to make everypony an immortal alicorn.
Yep, there goes the neighborhood.
We get it, Eldrae. You're the cool kids on the galactic block, you're smart, you're tough, you've got all the best toys, and when you stick your noses in other sophs' business it usually fixes problems they didn't even know they had.
Could you just stop acting so darn smug about it!?
3954734
Now, now. Let's not jump to too many conclusions.
After all, the eldrae might be about to become friends with the people who control the sun, can play pool with planets, micromanage the weather, casually turn deserts fertile, perform major feats of matter editing by thinking about it, pace up and down by teleporting, etc., etc. It ain't all going to be one way, not by any means.
(Also, I will promise in advance now that everypony will not, in fact, become immortal alicorns. In fact, I'll go so far as to say that the canonical alicorn count will not be exceeded in the course of the story.)
3954771 Ha! Good point.
Well, regardless of whether you cover it in-story, I'm smiling at visions of dragons and Vonnies alike experiencing similar consternation when they find out what this cultural exchange will mean for their old neighbors. "They were insufferable enough before they were able to [insert transplanted capability here]!"
Came across this Punnett square once upon a time that produced a nice stable arrangement of phenotypes through a rock-paper-scissors dominance pattern (or as the ponies would say, hoof-feather-horn. Hoof bops horn, horn plucks feather, feather tickles hoof.)
And we have a nice illustration of pony evolution through the generations here, to add to the genetics headcanon pile.