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The Genetics of the Pony by theaceofspadez The Genetics of the Pony by theaceofspadez
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.

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)
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Chersema Featured By Owner Nov 17, 2014
"Holy Crap!" I hear you cry out. 

That line cracked me up so much. Good guide.
BirdOfDeStars Featured By Owner Sep 25, 2014  Hobbyist General Artist
Rainseed Featured By Owner Jun 11, 2014  Professional Digital Artist
Is it alright to refer to this for genetic models for original species on it's function and structure while giving credit to you for it?
theaceofspadez Featured By Owner Jun 11, 2014  Hobbyist Digital Artist
Sure, I suppose that's fine.
Rainseed Featured By Owner Jun 12, 2014  Professional Digital Artist
Thank you<3
Paradoxelle Featured By Owner Apr 3, 2014  Student Digital Artist
You claim that Applejack is possibly an Alicorn Earth pony because of her strength, however, is it possible that her strength is developed just from her sheer hard work and dedication, which we saw was a huge part of her personality pretty early on in the show; out of the main six, with her physics and reality breaking behavior, wouldn't Pinkie Pie be the Earth Pony most likely out of the 2 to have the Alicorn gene? Or do you think it more likely Pinkie Pie's awesome but strange traits to be signs of another gene altogether? I can see Twilight, obviously, because super glowy eyes level of magic from a young age and last season of course, and Dash isn't too much a stretch because she can do a rainboom, something no other pony can do, just as Celestia and Luna raise the sun and moon ALONE, something no other pony can do. Plus Fluttershy screams recessive earth pony with pegasi genes. Don't get me wrong, I love Applejack...she is one tough cookie as the breadwinner entrepreneur and main matriarch of the Ponyville branch of the Apple Clan, but surely it's all that farm work that has her so strong.
Morticia-Lynne Featured By Owner Mar 24, 2014  Student Writer
I'mma jussgonna show this to my science teacher, mkah?
Rainseed Featured By Owner Feb 11, 2014  Professional Digital Artist
Definitely the best work and explanation out there, do you mind if people refer to this when breeding pony types?
theaceofspadez Featured By Owner Feb 17, 2014  Hobbyist Digital Artist
Not at all, that's why I made it!
wanderingbishop Featured By Owner Jan 20, 2014
I'm thinking that forcing the expression of the Pegasus gene fits on a thematic level - Celestia didn't fundamentally change Twilight, she drew out what was always in her to begin with.
BratzDArkRock Featured By Owner Jan 16, 2014  Hobbyist Traditional Artist
I love genetics. And this was very interesting to read. I'll take some time to think about it.

Thanks so much for posting it on DA!
mojomcm Featured By Owner Dec 25, 2013  Hobbyist Digital Artist
This is very well thought out and excellently presented. Cutie Thumbs Up 
User1997 Featured By Owner Aug 11, 2013
WHOA! Now prove their existence, and you will receive the Nobel Prize!
Snowpup22 Featured By Owner Aug 16, 2013
and alot of people's respect :P :iconpinkiepieplz: :iconpinkiepiefillyplz:
zdsc28 Featured By Owner Jul 24, 2013
mine is a simple pegasus with alot ,wait,WAT
MINE IS A simple unicorn with 5 talents
AskPastelSkittlesMLP Featured By Owner Nov 30, 2013  Hobbyist Digital Artist
There can only be one
Zaurra-WolfMaiden Featured By Owner Jun 5, 2013  Hobbyist General Artist
Ponies + science= 20% cooler
Polliniti Featured By Owner Apr 8, 2013
Sweet job!
-My oc is officially confirmed to be an Alicorn Pegasus-- :floating:
Thanks for the theorem
ILoveChocolateMore Featured By Owner Apr 7, 2013
I just have one question- why isn't there a separate allele for earth ponies? I mean, in your theory, you show that the only effects of the alleles(As far as I understand) are either the existence or absence of horns and/or wings, and, in the case of the alicorn allele, the enhancement of one's race's strengths. However, it has been hinted in the show that earth ponies are naturally stronger and, as you said yourself, have a special connection to nature. Unicorns and pegasi do not usually exhibit these traits, so why don't earth ponies have their own allele.
Also, I have another question. I might be completely wrong on this since I have no idea on how genetics work, but here goes- Wouldn't a ppnnaa or a PPNNAA pony turn out to be a weird mutant of sorts due to incomplete domination? Again, there is a big chance that this doesn't make any sense, but I just want an explanation on this since I don't really get it.
theaceofspadez Featured By Owner Apr 9, 2013  Hobbyist Digital Artist
There isn't an allele for earth ponies since the nature of my theory is that each allele, when present as capital (P, N, A) will specifically call for the presence of some actual feature/trait. Since what physically categorizes an earth pony is the fact they have neither wings NOR a horn, there's no physical feature for an allele to call for the development of. In the case of unicorn/pegasus, they have a horn/wings that had to develop at some point. Essentially, earth ponies "missed out" (meant in the best of ways) on getting wings or a horn, and I don't believe the "special connection to nature" is genetic (perhaps it naturally develops since they don't have to worry about flight, magic, etc).

As to your second question, it's possible that, for example, PP NN AA would give some co-dominant result. But, Codominance is a situation that arises with specific alleles on specific genes, for example in the human genome. I'm simply saying that the P, N, and A alleles function "normally" in the dominant/recessive fashion, and cancel each other out when they are both dominant (with the exception, of course, when paired with aa).

Hope this clears it up!
Mawxee Featured By Owner May 27, 2013
Just to make sure I get this straight.
- Pegasus and Unicorn genes work like a set of scales where the dominant genes are of equal weight. (I believe "codominant" is the correct word for this.)
- If they cancel each other out, we get an Earth pony.
- Alicorn genes act as a booster:
AA makes basic ponies,
Aa makes ponies with boosted power and
aa bypasses the cancelling effect and allows both mutations if they are present and at equal strength.
AndytheB-Artist Featured By Owner Feb 21, 2013  Hobbyist
So, what would happen if a Pegasus pony gave birth to a Unicorn or Earth Pony and it fell out of Cloudsdale?
theaceofspadez Featured By Owner Feb 21, 2013  Hobbyist Digital Artist
Hah never thought of that. There'd have to be some way of keeping them from falling, then they'd probably have to grow up on the ground.
ambergem16 Featured By Owner Feb 5, 2013
timstro59 Featured By Owner Jan 21, 2013
That makes absolutely perfect sense.
theartgirl19807 Featured By Owner Dec 29, 2012
Crisy101 Featured By Owner Dec 8, 2012  Hobbyist Traditional Artist
This is awesome!!! And it makes so much sense, I love it!!! And I plan to make a video about how this might apply to your shipping pairs kids. After all what would be the purpose of this chart if you couldn't apply this to your shipping pair lol. Don't worry I will credit you when I do. I plan to also do a video about the colors of a pony (after reading this, I came up with that), but it would still be awesome if you could do that. Of coarse only if you want to. But I digress awesome work!
ShrapnelLeader Featured By Owner Nov 23, 2012
God, I love this fandom. Very well done!
sneezefeatherWarrior Featured By Owner Nov 14, 2012  Hobbyist Traditional Artist
This... is very interesting. In a good way! I am so happy that you were so dedicated to mlp: fim! This is an amazing theory. Bro-hoof! /) (\
Charanty Featured By Owner Sep 27, 2012
This explains how baby Cakes are Pegasus and unicorn respectively.
Deep-Fried-Love Featured By Owner Sep 26, 2012  Hobbyist General Artist
GingaNinja100 Featured By Owner Aug 16, 2012  Hobbyist Traditional Artist
This is truly fascinating! You should next try a genetics chart of pony mane and body colors! Also, I would like to see one of dragons, because Spike seems to be a rare type of dragon, with no wings and the ability to transport messages via flame.
Mawxee Featured By Owner May 27, 2013
Maybe he is simply too young to sprout wings yet. Think Charizard.
As for the messages, that might be a spell. o.o
Ryeio Featured By Owner Oct 11, 2012  Hobbyist Traditional Artist
Spike wingless spyro?
KitsiesPanda Featured By Owner Aug 11, 2012
I feel like a complete nerd, but I like this a lot~ Very nicely formatted, very good theory.
EqFAzrael Featured By Owner Jun 24, 2012  Professional General Artist
Then somehow, Princess Celestia lost her a gene, so she lost the ability to use the elements of harmony...
theaceofspadez Featured By Owner Jun 24, 2012  Hobbyist Digital Artist
Of course, in addition to requiring a specific allele, the Elements bond to a particular pony and are only usable by that pony... that's pretty much directly from the show.
Tretharien Featured By Owner Jun 21, 2012
Good stuff. Always like seeing some science put into any tv show, especially one I like to watch. I was going to suggest incomplete dominance or dual expression for the advent of winged unicorns, but your use of an amplifier gene is pretty elegant in its simplicity. Well done Brony!
Dreams-hold-Ambition Featured By Owner May 23, 2012  Hobbyist Writer
You know, I wonder exactly how a pony's mane and coat color are determined. (Since None of the members in Pinkie Pie's family are the same color)
PrincessLunaFTW Featured By Owner Jun 20, 2012  Hobbyist Writer
It probably depends on the brew of magic they have stored in them. If you haven't noticed, there seems to be an abundancy of pink earth ponies, white unicorns and blue pegasi. Maybe it has something to do with that?

Shooting in the dark here.
theartgirl19807 Featured By Owner Dec 29, 2012
I think it's on a different chromosome than the p,n,and a genes, but they might be connected, maybe interlocked in some way?
Shown below:
/\ /\ /\ /\
/ \ / \ / \ / \
/ \/ \ / \/ \
/ \/ \
P, N, and A Coat Color
See what I mean? Maybe the chromosomes are fused together, but only mildly so the color is not determined by species and there is still chance.
I take honors biology. :)
PrincessLunaFTW Featured By Owner Dec 29, 2012  Hobbyist Writer
So basically what you're saying is, in unicorns the white coat color is dominant over say yellow, and with earth ponies it's pink and pegasi it's blue? I see... But wouldn't that mean there would be an even greater number of blue pegasi and so on?
theartgirl19807 Featured By Owner Dec 29, 2012
Well, crossing over still provides variations, for one.
But secondly, go back and watch one or two episodes where there is a big crowd, like the one about nightmare night, the season 1 finale, or Winter Wrap-Up. There are many different coat colors, and there are only two possible ways to include that many colors.
ONE: The dominant and recessive traits vary between family. (For that to work, the families would have to be interbred. Eew.)
TWO: There are subs for dominant and recessive, like, FOR EXAMPLE, Asub1 or asub1. That could work.
And did you read the other post I did right below this? I forgot to check the comment before adding it. Maybe it will clear up a few things?
PrincessLunaFTW Featured By Owner Dec 31, 2012  Hobbyist Writer
1: Inbreeding is actually really common in horse breeding, especially with thorough breds. Maybe in Equestria, it's as common a sight as filly-foolers and colt-cuddlers.
2: I'm not sure I quite understand that, I've never heard of subs. xD;

And sorry, but I don't see the post you're talking about. >~<; Maybe you could c/p the reply you mentioned?
theartgirl19807 Featured By Owner Dec 31, 2012
1. It's actually above this, look for all the slashes (don't mind them, or the line below them)
2. Subgenes are actually very common in alleles where there are more than two phenotypes. It's common in flowers that are both red, white, and pink. Google it, but it's in most genetics textbooks.
theartgirl19807 Featured By Owner Dec 29, 2012
Just realized deviantart comments don't do that. LAWL. But it's just like a Venn diagram, but only with two X's. At least, that's my theory. :D Hope you like it!
That was my honors biology talking. O.o
Lyfin Featured By Owner May 10, 2012
Holy shit...
xx-thisisme-xx Featured By Owner Apr 14, 2012
I linked this in a brony Facebook group I'm in when someone commented that Blueblood isn't an alicorn (or winged unicorn, by your definition) :) However I would like to point out that the filly alicorn from Lesson Zero is referenced at the inheritance chart, but no picture is given, just "this winged unicorn". This seems to be a minor oversight :P Great job though!
MHmania Featured By Owner Mar 22, 2012  Hobbyist Digital Artist
I did't understand half of it but OMG so awesome. I enjoyed it anyway.
Inko21 Featured By Owner Mar 15, 2012
I do have a few questions.
Where did Discord come from then?
Is he capable of producing offspring?
Dose he even follow these genetics?
Or simply is he just a "god?"

I lean more toward "god."
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November 27, 2011
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