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January 15, 2012
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Title: A dissertation on the hypothetical genetics of the Cake family

There has been dissension among the ranks of bronies as to whether the Cake parents, who are Earth ponies, could produce a pair of fraternal twins with one being a pegasus and the other a unicorn, given only one distant ancestor carried a single representative phenotype of each on either side.  

I have developed a plausible pattern of inheritance to explain this seeming incongruity.

Let's say that pegasi and unicorns were genetically designed, using earth pony as the genetic base, by the alicorns playing god on the mythical continent of Atlantis.  The easiest way to add the genes to the earth ponies would be to design an artificial chromosome carrying all the needed genes.  Then this chromosome's expression could be triggered by a special transcription factor integrated elsewhere in the genome, likely tied via a promoter to other developmental genes.  My bet is the BMP-Bcat-Wnt signalling system, since horns and wings both require skeletal augmentation and early patterning.  

But, you wouldn't normally want a pony to end up with both, so one could also include suppressors on each of the types of artificial chromosomes, such that if any pony ended up with both types of chromosomes and promoter elements, the supressors would shut down the expression and the offspring would be an earth pony carrier of both traits.  Also, if out-breeding with Earth ponies occurred, the different chromosomes and promoters could become separated (aka Au=unicorn artificial chromosome, Pu=unicorn-specific promoter element.  Unicorn genotype-phenotype correlation= AuPu.  Earth pony base:  B=base chromosome Q=null carrier for artificial chromosome.  Earth Pony genotype=BQ.  Assuming they are homozygous for each trait and crossing, you end up with an F1 genotype Au/Q Pu/B.  

Successive generations would further dilute this background.  Assume also the same rules apply for Pegasi Ap/Ap Pp/Pp homozygous genomes: F1 earth pony cross yields Ap/Q Pp/B.  

We can add in the assumption that at some point, any one of the Cake's direct relatives might have reproduced with another Earth pony carrying a promoter or artificial chromosome from the opposing genome. Now, taking into account that each type of artificial chromosome carries the suppressor for the other trait AND that the promoters are specific to each artificial chromosome, we can end up with these diploid genotypes in Mr and Mrs Cake without their developing any pegasi or unicorn traits:  Ap/Q Pu/B  and Au/Q Pp/B.  

Following gametogenesis, these 8 haplotypes can be generated: Parent 1: ApB, ApPu, QPu, QB  Parent 2: AuPp, AuB, QPp, QB.  

As you can see, with such combinations available, there is the chance for the twins (being fraternal rather than identical) to end up with the correct combinations to allow expression of either unicorn or pegasus:  ApB/QPp= heterozygous pegasus, QPu/AuB= heterozygous unicorn.  The raw statistical probability of each genotype is 1/4 x 1/4 = 1/16, which is actually not at all unlikely.  

In my genetics lab, we've done mating with mutant mice for 3 genes with a probability of 1/32, and still end up with some of the combined mutant genotype in roughly every other litter of mouse pups, averaging 8-10 pups/litter.  So, in conclusion, should the genotype function as described in this paper, it is entirely possible for the Cake foals to exhibit the unicorn and pegasus phenotypes despite having earth pony parents.

Soooo, Celestia... is this enough for my PhD in Pony Genetics?  ;3
Given the preponderance of dissent within the community of bronyism elicited by the recent episode of My Little Pony: Friendship is Magic, regarding the seeming implausibility of the phenotypes of the twin foals of Mr. and Mrs. Cake , I felt it my duty to offer a brief, logical hypothesis describing a genetic inheritance scenario which would indeed allow for just such a resultant familial pattern within the realm of statistical probability. My Equestrian scientific adviser concurs. *nods to a life-sized Twilight Sparkle plush* We both hope you will find that my dissertation enlightening.
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lamphobic Featured By Owner Dec 28, 2012
O.o Can somoene dumb down the complex terms like "representative phenotype", "artificial chromosome ", "chromosome's expression", "special transcription factor", "genome", "promoter", "BMP-Bcat-Wnt signalling system", "suppressors", "diploid genotypes", "haplotypes" and whatnot for those of who haven't taken a class that covers this sort of topic? Please?
Charlesdeleroy Featured By Owner Dec 29, 2012
Oh dear... it would take several pages of explanation to cover all that.

Let me see if I can clarify.

Representative phenotype = the physical form dictated by the expressed genotype

Artificial chromosome = A chromosome built by scientists rather than being a natural one.

Chromosomal expression = the activation of the genes of that chromosome, producing mRNA, miRNA and proteins from translation of mRNA by the ribosomes in the rough endoplasmic reticulum after the mRNA is transposed through the nuclear membrane (watches you brain explode) Oh dear, I knew that might happen.

Genome = the entire set of genes comprising an organisms DNA.

promoter = a small DNA sequence, frequently located slightly in front of the coding region of a gene sequence, which serves as a binding site for proteins involved in transcription (the production of RNA)

BMP-Bcat-Wnt signalling system = One of many protein signalling cascades which are crucial for various aspects of embryonic development. They serve as master control switches for regulating hundreds or thousands of other genes. BMP-Bcat-Wnt functions in the development of the skeletal system, heart, limb development, formation of the neural plate derivative and neural progenitor line, formation of mesoderm and mesoderm-derived structures such as parts the middle and inner ear.

Suppressors = genes which produce proteins or miRNA (micro RNAs) which can reduce the activity of other genes either by directly binding to a region of the target gene or preventing translation by binding to the mRNA or promoting ubiquitinization (a tagging process marking an mRNA for degradation by RNases)

diploid genome = The normal number of chromosome copies in most animals is 2 sets. Each particular chromosome exists as something of a matching pair in cells. X and Y chromosomes are an example. A female has a diploid XX and a male has a diploid of XY. The pairs of chromosomes segregate, one set to each side, of a dividing cell. Then a new matching set of chromosomes is created from the half set (known as the haploid number) before the cell completes division. Humans have a haploid number of 23 and a diploid number of 46.

Haplotype = The genotype resulting from possessing half the diploid number. Contains 1 of each type of chromosome. Gametes consist of haplotype genomes, as they have haploid chromosome numbers. human sperm = 23, human ovum = 23. Fusion into zygote results in diploid 46. Haplotype is a term most commonly used when speaking about a limited number of genes. For instance, a gametocyte before meiosis might have the genotype Hh for a Hair gene (H being dominant, h being recessive), after meosis, the haplotypes of the resulting gametes would be either H or h.

lamphobic Featured By Owner Jan 12, 2013
Specifically why does everything have two sets of genomes and why does these one have one set?

"Unicorn genotype-phenotype correlation= AuPu"

"Earth Pony genotype=BQ"
Charlesdeleroy Featured By Owner Jan 13, 2013
All animal chromosomes come in homologous pairs. BUT they may not have the same variants of genes on each one.

Plus, they need to have both the activator gene and the main pathway initiator gene for the unicorns and pegasus traits.

For the Earth ponies, in the space of those genes, they have variants B and Q, which result in a base Earth pony phenotype.
lamphobic Featured By Owner Jan 12, 2013
Thank you for the explanation I (think I) understand this much better now.

Why does everything have two sets of genomes?

EX. "Pegasi Ap/Ap Pp/Pp homozygous genomes", "Ap/Q Pu/B and Au/Q Pp/B", " ApB/QPp= heterozygous pegasus", etc...
Charlesdeleroy Featured By Owner Jan 13, 2013
These are the gene pairs which are the sum of the genes carried by the pairs of chromosomes.

This assumes that the activator and pathway initiator genes are on different chromosomes, which they must be for the mixing of the genes to work and result in non-expressing carriers. If they were on the same chromosomes, only cross-over events would result in variants. You could say that unicorn and pegasus only result from homozygosity and thus the carrier of only one unicorn or pegasus chromosome would be an Earth pony.

But then for the Cake twins to be born, both parents would have to possess a unicorn chromosome and a pegasus chromosome. It's possible, since we aren't given the whole family history, and the odds aren't bad: 1/2 of the offspring would be an equal number of pegasi and unicorns. Now, this would also mean alicorns are due to a translocation which splices all the traits onto a single chromosome. However, since this unusual phenotype also grants large physical size, massive increases in magic, and immortality, it's clear that alicorns are quite a bit more complex than merely splicing a few genes together.

Hence, why I stuck with my idea that the entire race was engineered with these activators and repressors; alicorns then being the result of translocational mutation merging the artificial magical pathways, which would be tapping into the magical field of Equestria via some manner of very intricate biochemical structure acting at the quantum level to channel magic (perhaps catching it akin to the way chlorophyll traps light energy), resulting in an exponential increase in abilities.
smunsch Featured By Owner Jul 12, 2012  Hobbyist General Artist
I would actually like to see a dissertation on the genotypic and phenotypic variances among ponies, and see if we can't establish some sort of family tree. DJ Pon-3 (aka Vinyl Scratch) currently has unknown parents, but I don't doubt she's related to somepony else that's visible as an extra. Her coloring resembles Twinkleshine's quite a bit; there may be a relationship there.
Charlesdeleroy Featured By Owner Jul 15, 2012
Given the Cake's genetics, I'd say anything is possible family relation-wise unless it's ruled out by canon.
Kelcius Featured By Owner Jan 22, 2012
Common Pegasus Ancester

↓ ↓
GGGGgrandma First cousin Thrice removed for CCGaunt
↓ ↓
GGGgrandma Second cousing twice removed for CCGaunt
↓ (pegasus)


Grandma---------------CC Gaunt


Cup Cake
Charlesdeleroy Featured By Owner Jan 22, 2012
Or aliens.

The Greys did it all! *hides in basement with foil hat*
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