Pony Genetics · 5:35pm Dec 23rd, 2017
Supplemental reading material for Cat's Cradle, or
Pony Genetics
There have been several articles on the topic of pony genetics since the Baby Cakes episode in season 2. Most of them are laughably flawed, or have a gross misunderstanding of how genetics work.
The Baby Cakes episode gave canon evidence that pegasi, unicorns, and earth ponies were not different species but were, instead, different races of the same species, capable of interbreeding. And that two ponies of one given race could have foals of another kind due to genetic phenotype.
"My great-great-great-great grandfather was a unicorn, and Cup Cake's great aunt's second cousin twice removed was a Pegasus. That makes sense, right?"
— Mr. Cake explaining why Pound Cake and Pumpkin Cake are a pegasus and a unicorn respectively.
And as our Lord and Savior confirmed,
"[Ponies] were all born from the usual, standard, run-of-the-mill, mammalian reproduction."
- Lauren Faust (praise be unto She!)
But before we get into the interesting stuff, a quick overview of Genetics 101.
Genes are contained in the chromosomes. For each gene there can be one or more alleles, that is "variants" for the expression of the gene. Each chromosome can have a different allele for the same gene. This can have a dominant/recessive relationship.
All that means is that a dominant allele will override a recessive one. It is NOT an indication of the strength of that trait. Often, the dominant allele will be the absence of that trait. And this is important!
I have made a Punnett Square that I feel best represents the races of ponies we see in Equestria as we currently understand it.
Here are the rules, as best as I can figure from my research:
1. For a Unicorn or Pegasus trait to be visibly present, it requires a pair of recessive alleles of that type.
2. AND it must be the ONLY pair of recessive alleles in the sequence.
3. Otherwise the genes conflict and cancel, and the result is an Earth pony.
4. The ONLY exception is an Alicorn: eeuupp All recessive alleles equally present.
47 Earth (Orange)
8 Unicorn (Red)
8 Pegasus (Blue)
1 Alicorn
This is an example of all the possible outcomes of two perfectly heterozygous ponies, EeUuPp x EeUuPp. In this very specific example, these parents would have a 1 in 64 chance of having an Alicorn foal.
So why are there not 1 in 64 ponies in the population an Alicorn? Because this table is not an accurate representation of the population's gene pool. It is actually weighted and skewed by region and culture. Think about it this way: Just because 1 in 6 humans on earth are Asian, does not mean that any given couple has a 1 in 6 chance of having an Asian child. That's bad statistical logic.
Two ponies on a date in Cloudsdale would be pegasi. They would have to be, in order to even be there. So the population is going to be skew toward having purebred Pegasi foals: EEUUpp. Purebreds have purebreds, and that is how it works by these rules, and in nature at large.
And not to sound racist, but as forward thinking as we like to think we are with cultural diversity, the simple reality is that white people tend to date white people, blacks date blacks, Asians date Asians, etc.
Even with the relatively small sample size of canon parents that we've seen, this is generally the case among ponies as well.
These factors further preclude the possibility of an Alicorn foal, which is a perfect mix of all the races' recessive alleles.
Lets look at some canon precedents. First, let's look at the Cake family.
As Carrot Cake stated,
"My great-great-great-great grandfather was a unicorn, and Cup Cake's great aunt's second cousin twice removed was a Pegasus. That makes sense, right?"
This just further solidifies the idea that dating outside of one's own race is, if not frowned upon, at least rare.
BUT we can use this example to examine the Cake's genotypes:
In this case, whether they each have EE, Ee, or ee is irrelevant. If they were both perfectly heterozygous, we could just reference the table at the top. But as we've seen, while it is mathematically possible, it is very unlikely that they are, especially given Carrot Cake's description of their family histories. For simplicity we can assume EE for both.
Of the 16 possibilities:
10 Earth
3 Pegasus
3 Unicorn
For them to have fraternal twins with one of each is about a 1 in 30. (The probability of a mare having twins at all notwithstanding). But still, WELL within the realm of the possible.
Either that or Mrs. Cake is just a cheating hoe. Much simpler.
Which brings us to Alicorns and the curious case of Flurry Heart.
Daughter of the unicorn, Shining Armor and Princess Cadance, an Alicorn.
But as the Crystal Heart Spell explains, Cadance was born a pegasus and ascended to become an Alicorn like Twilight Sparkle.
One could assume that the transformation was a result of a magical change to her DNA. But what would a spell like that even look like? Hmm...
We have only two possibilities.
1. Cadance was a heterozygous Pegasus, and her ascension did not change her DNA.
or
2. It did.
Here are the two possible tables, based on the rules of Pony genetics, and what we know about each of them.
At best, Cadance and Shining had a 1 in 16 chance of having an Alicorn. And Celestia and Luna were right to be surprised at the event.
If Cadance's DNA was altered as a result of the process, the odds of them having an Alicorn foal become 1 in 4!
That is entirely within the realm of a couple of ponies to have!
But even Celestia can't just go in and start making huge changes, re-arranging DNA. That's how you end up with Cronenburg ponies.
For a pony to ascend to an Alicorn via a magical alteration to their DNA, they would likely have to already be very close to the right combination.
Of course, somepony would have to be overseeing the process of the selective breeding for generations to ensure such an outcome. 
!["[Ponies] were all born from the usual, standard, run-of-the-mill, mammalian reproduction."](https://derpicdn.net/img/2012/10/1/111511/full.png){kind=link}
ooooooooooh, neat
Let's just take a moment and appreciate the concept of Cronenburg ponies.
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If you insist.
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unf
Tl:DR miss Cake is just a cheating hoe, much simpler.
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I actually meant to have that part in my post!
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It is not racist to state a fact. For example, on the intelligence hierarchy, especially in genetics, blacks are below whites, who are below East Asians on overall intelligence. That's fine.
It's the actions of a person using said information that determines if it's racist.
And I know there is going to be a knee jerk reaction to those statements, but I will only say it's OVERALL intelligence over billions, not that there can't be exceptional individuals or civilizations.
Celestia is pro-eugenics.
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Okay, you just gave me my nightmare for the night.
Also, thanks for the blog post too.
This brings back memories of high school biology. This however, is a lot more interesting
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Nice~
Head canon accepted
Muh GENETICS.
Hmm just to say... the genes are contained in the chromosomes.
For each gene there can be one or more alleles, that is "variants" for the expression of the gene.
This can have a dominant/recessive relationship.
Each chromosome can have a different allele for the same gene.
So it's the allele that is Dominant or Recessive, not the whole chromosome.
In the case of the sex chromosomes as the Y is shorter than the X it happens that some genes are present ONLY on the X chromosome and so you get expression of a recessive gene even if the father had the dominant version
4757663 I've said it before. I have the best fans.
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Wait. What about thestrals? Not to sound like an ass. Is there not enough data?
This is the take on pony genetics I've used in my own story building and brainstorming:
orig00.deviantart.net/53af/f/2017/359/f/1/ponygenetics2_by_wodahseht-dbxrlk4.png
(Click to visit full version if hard to read.)
Basically, each pony's "race" is based off four gene markers. Each parent donates two points. Mother donation attaches at front, highest multiple of a marker wins if multiple of same present, and first marker to appear in the full set wins in case of ties. This was best way I could figure to account for multi-generational carrying.
I also like to think of the Mane6 as the following gene setups:
Twlight => UUUU (With Celestia altering to AAUU or AUAU during the ascendance.)
Applejack => EEEE
Rainbow Dash => PPPP
Rarity => UPUP or UPPU
Pinkie => EUEU or EUUE
Fluttershy => PEPE or PEEP
I came to this setup based on fact that Twilight, Applejack, and Rainbow Dash seem to epitomize their sub-specie to an extreme degree. Rarity took to weather magic with no issue during cutie-mark mix-up (it was just her fashion sense that was screwing things up for her) so I like to think she has pegasus markers in there. Pinkie has a lot of "wild magic" I like to think of as being because of the strong unicorn contribution. And Fluttershy has a strong connection with nature and animals I think of as being tied to earth pony markers.
In the case of Flurry Heart, I think that Cadance (AAPP or APAP) donated 'AA' and Shining (UUUU) donated 'UU' to result in an alicorn child.
Edit:
* Updated to add bat ponies: A = Alicorn, E = Earth Pony, P = Pegasus, B = Bat Pony, U = Unicorn
All I got out of this is a lot of Big Mac quotes.
Eeup, eeeuuup, eeuup.
So thanks for that.
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Unless we see a canon pony/ bat-pony hybrid, I will continue to believe that they are a separate species, like Zebras.
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I didn't have bat ponies in the chart until after Admiral's comment. Original chart was: orig00.deviantart.net/6f26/f/2017/358/e/b/ponygenetics_by_wodahseht-dbxrgrk.png
Though I'm testing a rework of it completely based on your post.
So, I did a serious revamp to my headcanon based on this blog. Posted the results here if you're interested. I'd welcome your thoughts if you do give it a look.
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You're correct, facts are not inherently racist. The problem is that the "fact" you followed that up with is completely wrong; there is an entire Wikipedia article discussing how the social conception of race has very little basis in genetic reality. In point of fact, sub-Saharan Africans have more genetic diversity than any other group on the planet, and Africa is the most genetically diverse continent: all other groups in Africa are more closely related to each other than to sub-Saharan Africans (both of these are as expected from the single-origin hypothesis of human evolution). Arguing in favor of a single "black race" (much less any race-based "intelligence hierarchy") is specious; it is a myth perpetuated by racist individuals and those who are too ignorant to know better (these are not necessarily exclusive to each other - quite often, racism cannot persist without ignorance).
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I can also follow that up with Wikipedia not being a reliable source at all. You do have ideological groups trying to push certain ideas onto it in order to conform to a narrative, especially when news outlets are ideologically on their side. People have claimed long standing bias, especially from certain editors or trying to twist the rules for their own purposes, though reports are scattered. For example:
https://www.newyorker.com/tech/elements/a-feminist-edit-a-thon-seeks-to-reshape-wikipedia
http://dailycaller.com/2014/02/02/wikipedia-is-very-masculine-so-feminists-pledge-to-fix-it/
https://hbr.org/2014/12/wikipedia-is-more-biased-than-britannica-but-dont-blame-the-crowd
I point to Feminists because they're easy to find out and they're notorious for believing in certain things like the meme "gender is a social construct", despite trying to weasel their way around certain concepts like sexual dimorphism.
Not saying you're wrong or not, and I need to read up to confirm or deny your evidence, but I wouldn't use Wikipedia as a primary source. DuckDuckGo would be more reliable. (Google is well known to have a bias too.)
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There you have it from the lips of Lauren Faust (praise be unto she).
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Yeah, a few days after my last comment I'd revamped chart to add batpony as separate, with minor modification of requirement for alicorn to account for that, but never bothered to put it online with life and all. In the end, I doubt I'll ever actually use all of it, so it got shifted to the side.
Personally I see it all ponies have the potential to be alicorns, but it takes some form of magical event, usually centered around some personal epiphany to trigger it. Of course, one could push Probablity say with Chaos magic, or more horrifically some sort of sacrifice, but such a thing leaves the pony a warped individual. Of course since such a thing would have to be done voluntarily in those cases, the individuals mental state is hardly all that stable to begin with
Or it was the result of some otherworldly power... some ham fisted idiot god who seemed more obsessed with... oh, I don't know, selling some sort of shitty toy to either children or obsessed weirdo's then they are worried about ham fistedly shoving a narrative rather then telling a story.
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But the case of Flurry Heart being born an Alicorn throws out the 'becoming an Alicorn based on merit' theory.
Also, Cozy Glow's self-accession should be dismissed out of hoof as a temporary magical aberration.
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Well, it can just happen on its own, or by being exposed to some arcana mcguffin, or while stickings one schlong into a zebras eyesocket while she sings the Russian national anthem, or just standing around picking ones nose, which is pretty impressive when one has hooves
As I said, all ponies have the potential to be alicorns, but the chance of that happening are slim. Genetics, of course, do contribute to it, but Flurry Heart had more odds of being a born a 70 year romanian rug slapper then she did an alicorn