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MLP: Pony Genetics by CocoaNutCakery MLP: Pony Genetics by CocoaNutCakery
So there have been many attempts to explain pony genetics, but all of them fall short when considering what we've seen in the show and, quite frankly, how genetics work.

So I went ahead and took a shot at it.

Let me know what you think.

Oh, and as far as the unicorn horn and pegasus wings go, those are part of what is blocked. If Fluttershy had inherited all the genes she did except for the ones that determine pony type and got EE for those, she wouldn't have survived. Growing the horn and wings would take considerably more strain on the fetus than growing just one of them with the Earth Pony magical abilities.

Edit: I didn't explain this in the big... thing... up there, but a lot of Fluttershy's character traits (shyness, possible instability, etc) could theoretically be traced to her body putting less energy into them and instead directing the energy towards increasing her tolerance for magic and growing wings instead of directing energy towards certain parts of her brain development (such as hormone receptors).

Edit2: Please keep in mind that Mr. Cake is not a geneticist. He should not be considered an expert on such things. Remember: Just because a character says something does not make it canon. There are such things as misinformation, lies, and mistakes.

Edit3: Just so there's less of a chance of me getting asked this again: The Cake twins are UU (Pegasus) and PP (Unicorn).
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:icontrinplays16:
TrinPlays16 Featured By Owner Nov 14, 2015
What would the genes be for an Alicorn?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Nov 25, 2015
Read the image.
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:iconeonorteashadowmaster:
EonOrteaShadowmaster Featured By Owner Jun 20, 2013  Student Writer
I'm impressed! Excellent work on this!
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:icongalacticpink:
galacticpink Featured By Owner Mar 18, 2013  Hobbyist Digital Artist
Question as a result of the Season 3 finale!

The implied to be unheard of ascension (I get the feeling at least Celestia has a specialized knowledge of this and knew of Twilight's potential to do, likely from her uncontrolled magic surge during her entrance exam) of a Unicorn to an Alicorn via the magic of friendship. Is there a genetic explanation for this, or is it just one of those things that can be passed off as the miracle of magic/friendship?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Mar 18, 2013
Well, I kind of have a theory about the origin of Alicorns, but it would kind of be a spoiler for Rise of the Legend.
Let's just say that Twilight is the only pony to have changed into an Alicorn without... outside influences.
As for how it worked, the spell just altered her genetic makeup, but--as is strongly hinted in the season 3 finale--it required the power of the EoH and could only work on the wielder of Magic.
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:iconuxileaf-senpai:
UxiLeaf-Senpai Featured By Owner Jun 27, 2013  Hobbyist General Artist
... If you aren't figuratively speaking, Princess Candace was a pegasus that learned the true sense of love, and was granted the Alicorn status.
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jul 4, 2013
According to the comics, yes. I'm working within the show's canon.
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:iconberrypunchrules:
BerryPunchrules Featured By Owner Feb 22, 2013  Hobbyist Digital Artist
I don't like the part about fluttershys rare genes. I really don't see how a unicorn and earth pony can produce an entirely different race, and based on the season three finale, maybe alicorns have to be created? Id like to see a gene explainer with mane and coat color.
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Feb 24, 2013
Well, mane and coat color would just be regular genetics. There's nothing particularly interesting about them specifically.

As for the producing an entirely different race, think of it like this: You have a device that emits three lights out the front, along with two bars that hook onto the device that each have two shades.

So you've got it like this:

RBY

And with one of the shades in front:

R--

With the other shade:

--Y

Now, if you take one random shade from each one, you could end up with the shade that blocks the yellow from the first and the shade that blocks the red from the second, ending up with:

-B-

An entirely different light.

As for the season finale, if you'll recall, that spell was one that Starswirl couldn't finish. In other words, the spell to turn a unicorn into an Alicorn not only required the unicorn to wield the element of magic (remember that the spell worked through the Elements of Harmony), but it also didn't exist for Celestia, Luna, or Cadence.

What don't you like about Fluttershy's rare genes?
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:iconberrypunchrules:
BerryPunchrules Featured By Owner Feb 25, 2013  Hobbyist Digital Artist
i don't like how it classifies her as different. i mean, it's just her personality.
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Feb 26, 2013
Except that it's been established, through Word of Faust, that empathy with plants and animals is Earth pony magic.
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:iconganondox:
Ganondox Featured By Owner Feb 10, 2013  Hobbyist General Artist
I think a better explanation is that there doesn't need to be any special gene, UU's are Pegasi and PP's are unicorn, but EE's are unviable. Or something.
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:iconthemanecobra:
TheManeCobra Featured By Owner Jan 29, 2013  Hobbyist General Artist
Ok, I just found this and I'm not sure if I have the right answers, so here are my questions.

1) My OC, Fallow Heart, is the offspring of two Alicons. He is an Earth Pony with a special ability that allows him to control or levitate some objects with ease, depending on his state of mind. He also has an earth pony sister, a unicorn brother, and a Pegasus brother. Is this possible?

2) Also, if my OC and Fluttershy were to have children, there would be possible earth pony offspring, right?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jan 29, 2013
1) Not by this explanation. Not in the slightest. There are other explanations that allow that (I can't point you to any right now), but not this one.
2) Well, if he was a standard Earth pony, being UP, and Fluttershy is UU, that would give a 1/2 chance of UU (unviable or rarely a pegasus with Earth pony traits, like Fluttershy) and a 1/2 chance of UP, which would be a standard Earth pony.
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:iconthemanecobra:
TheManeCobra Featured By Owner Jan 29, 2013  Hobbyist General Artist
I kind of sensed that the first question made little sense, and yet I asked it. Hehe, weirdness at its best. Anyways, thanks for the response.:D Might get back to you in a bit.
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:iconwoefulwriters:
WoefulWriters Featured By Owner Dec 21, 2012  Student General Artist
Are the genetics on my pony family tree correct? or should I fix it? [link]
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Dec 23, 2012
If you want to follow this explanation of pony genetics, it's extremely unlikely that Otis and Lily (BOTH being Earth ponies) would have had two Pegasi and two Unicorns (any other combination of partners, such as E/U, and that combination of children would be just as likely as any other combination). Additionally, they would most likely display some traits inherent in Earth ponies (think Fluttershy's fear of heights and talent with animals) as well as some... negatives as a result of growth energy being placed elsewhere (think Fluttershy's fears, her social anxiety, her occasional rage issues, etc).

But that's assuming that you want to use these genetics and you're not okay with such a low probability. It's not like this is official or canon and even if it was, there's no requirement to stick with it (there are a number of fan-made creations that contradict canon, either subtly or overtly).

All this is is a hypothesis about how genetics in the MLP:FiM universe work based on how genetics in our universe work and the information given in the show. You're free to create your own hypothesis or even dismiss the issue entirely if you so desire.

By the way, the person that does Slice of Pony Life had his (her?) own explanation of how pony genetics work, using an explanation involving polyploids (the explanation isn't... complete, but it might be something into which you'd like to look) and taking Mr. Cake's explanation as canon: [link] I did some digging into polyploids, and it's a... REASONABLE explanation, but I do take some issue with that explanation. That said, if you want to use an already existing explanation for two Earth ponies producing two Unicorns and two Pegasi, then that's an option there.
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:iconwoefulwriters:
WoefulWriters Featured By Owner Dec 23, 2012  Student General Artist
Thank you for the feedback. :D I'll check out the tumblr,and I will keep your theory in mind the next time I make a oc family.
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Dec 23, 2012
*Hugs*
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:iconwoefulwriters:
WoefulWriters Featured By Owner Dec 23, 2012  Student General Artist
:hug:
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:iconphantomxv1:
phantomxV1 Featured By Owner Aug 30, 2012
anything to help my story, OK the character was born from unicorns, she was born with no magic, but has the traits of an earth pony and still has a unicorns horn. explain, please and thank you
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Aug 31, 2012
Well, taking this, she would have magic. First, she'd have Earth Pony magic, but she'd also have Unicorn magic. Though perhaps her body does not prioritize some aspect that's important to Unicorn magic (actually, I have a theory about how magic works in MLP:FiM, but it'll have to wait until I'm back on schedule... though I guess I could explain it by saying that Twilight was VERY strong in magic to be that powerful without m/any friends) or something along those lines. Maybe she has trouble understanding how spells work or maybe her body deals with the excess magic by getting rid of it instead of being able to utilize it in a controlled way.
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:iconthenegaverser:
TheNegaverser Featured By Owner Aug 21, 2012  Hobbyist Digital Artist
Fascinating! I'm always interested when people take a scientific look at the world of ponies. Twilight would be proud!
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:iconthepegasusphantom:
ThePegasusPhantom Featured By Owner Jun 23, 2012  Student General Artist
Whoa! Thats so cool!
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:icontheblazer2048:
TheBlazer2048 Featured By Owner Jun 11, 2012
I'm afraid I'm not smart enoungh to understand...
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jun 13, 2012
One thing I've learned from tutoring math is this: The primary cause of not understanding is mental stress or tension. Just relax your brain matter and you'll be able to get it.
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:icontabberhatter:
TabberHatter Featured By Owner Jun 10, 2012  Hobbyist Digital Artist
Mind = Blown. :XD:
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jun 13, 2012
I do like blowing people's mind holes. :P

(That was a reference to How I Met Your Mother)
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:icontabberhatter:
TabberHatter Featured By Owner Jun 13, 2012  Hobbyist Digital Artist
Haha, nice, XD
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:iconscootalooinmyshoe:
ScootalooInMyShoe Featured By Owner Apr 12, 2012
Makes sense but does it explain mr and mrs cakes twins?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Apr 12, 2012
Yes. I explained how in reply to an earlier comment.
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:iconscootalooinmyshoe:
ScootalooInMyShoe Featured By Owner Apr 28, 2012
So uu was the pegasis baby and pp was the unicorn baby? So the pegasis would be part earthpony and the unicorn would also? Because unlike fluttershy the baby flew just fine. But I really can't see and other way to explain this so...You Win *yay*
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Apr 29, 2012
Well, you have to keep in mind that, in S2E02, Fluttershy proved that she can fly exceptionally well. It seems that it's more her fear of heights that keeps her from being an exceptional flier than anything else.

But when I get around to explaining my view of how magic works in Equestria, you'll get why their magic was stronger than some adult ponies.
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:iconpollosaurio335:
Pollosaurio335 Featured By Owner Feb 26, 2012
why is so complicated
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Feb 29, 2012
It's not that complicated if you know basic genetics and the principles of genetic blockers! I swear!
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:iconallyenderman:
AllyEnderman Featured By Owner Jan 29, 2012  Hobbyist Traditional Artist
I shall print this, and bring it into my Biology class, when I go back to school, on Tuesday.

We're starting genetics. xD
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:iconwanderingmagus:
wanderingmagus Featured By Owner Jan 14, 2012
rebuttal: Baby Cakes

:p sorry... how would you change it now?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Mar 30, 2012
PP and UU.

Those are the baby Cakes.

Of course, the lay pony doesn't understand the genetics behind unusual pony births, and the doctors sure as heck aren't going to bother to explain why Carrot Cake was incorrect in his assumption that it was their lineage.

By the way, their abilities seem far beyond that of the average pony of adult age, right? Well, my explanation of magic (which I have yet to post) explains that.

Sorry it took so long to reply, but I didn't watch the episode until this week. ...Yeah, I was a bit behind... but I'm all caught up now!
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Mar 30, 2012
By the way: I did point out that PP and UU are rare, but they are possible. Eventually, twins were bound to be born like that. And, again, an important factor in whether or not the PP or UU fetus survives is genetics. Carrot Cake and Cup Cake (were her parents planning to marry her off to someone with the last name of Cake or was this a case of incest?) just happened to produce the right combination of genetics that they had a chance of having their babies have a chance.

Basically, think of it like this: There's a .1% chance that the parent's DNA will be just right so that a UU or PP baby CAN survive, and a .1% chance that a baby conceived this way will survive. Since Mr. and Mrs. Cake have proven to have the genetics necessary, a PP or UU baby, rather than having a one in a million chance to survive, instead has a one in a thousand chance (and so twins have a one in a million that they will both survive, which is absurdly rare, but it does happen).

Randomly selecting a couple and seeing if their UU or PP baby will survive is a one in a million shot. If the couple can be proven to have the right genetics, then it's instead a one in a thousand shot.

Keep in mind that these are explanatory numbers and do not reflect the actual chances of a PP or UU baby surviving. Just keep in mind that, when the parents are proven to have the right genetics, that greatly increases the chances of a PP or UU baby surviving.
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:iconwanderingmagus:
wanderingmagus Featured By Owner Mar 30, 2012
interesting. So the Cakes took a big risk?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Mar 30, 2012
No.

Ponies don't choose what the genetic outcome of their children would be any more than we do. They didn't say, "Oh, let's try for one unicorn and one pegasus!" They tried for a kid and got one, the fact that they ended up with two and one was a unicorn and one was a pegasus was not their decision, it was random chance.
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:iconwanderingmagus:
wanderingmagus Featured By Owner Mar 31, 2012
they got lucky then :D
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jan 15, 2012
I haven't seen the episode yet, so I don't know.
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:iconcommissionangel:
CommissionAngel Featured By Owner Jan 14, 2012  Hobbyist General Artist
Strangely enough I get it O.O;
What about the genes that determnd the color of the mane and coat
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:iconlaurel3aby:
Laurel3aby Featured By Owner Jan 13, 2012  Student Writer
So.. if a Unicorn & Pegasus were to mate - the foal would be.. ?
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:iconcocoanutcakery:
CocoaNutCakery Featured By Owner Jan 15, 2012
Any of the three mane types.
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:iconlaurel3aby:
Laurel3aby Featured By Owner Jan 15, 2012  Student Writer
I see. Thanks :)
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:icongenericponyname120:
GenericPonyName120 Featured By Owner Jan 9, 2012  Student General Artist
I'm goin to have to favourite this so I can sit down and try to make sense of the information you have given me kind sir. Science = My weakest subject
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:iconisabelle-fox:
Isabelle-fox Featured By Owner Dec 29, 2011
i had to read that once, and then skim through it twice because parts of it made about as much sense as science class when i'm almost half asleep.
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:iconkd7sov:
kd7sov Featured By Owner Dec 29, 2011
Very well thought out, except for one point:

Why would it be just a single gene pair that determines pony type?
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